-
1
-
-
33847616971
-
Growth of novel protein structural data
-
Levitt M. Growth of novel protein structural data. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:3183-3188.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 3183-3188
-
-
Levitt, M.1
-
2
-
-
79953900818
-
Overcoming barriers to membrane protein structure determination
-
Bill R.M., Henderson P.J.F., Iwata S., Kunji E.R.S., Michel H., Neutze R., Newstead S., Poolman B., Tate C.G., Vogel H. Overcoming barriers to membrane protein structure determination. Nat. Biotechnol. 2011, 29:335-340.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 335-340
-
-
Bill, R.M.1
Henderson, P.J.F.2
Iwata, S.3
Kunji, E.R.S.4
Michel, H.5
Neutze, R.6
Newstead, S.7
Poolman, B.8
Tate, C.G.9
Vogel, H.10
-
3
-
-
77953005237
-
Making membrane proteins for structures: a trillion tiny tweaks
-
Baker M. Making membrane proteins for structures: a trillion tiny tweaks. Nat. Methods 2010, 7:429-434.
-
(2010)
Nat. Methods
, vol.7
, pp. 429-434
-
-
Baker, M.1
-
4
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Martí-Renom M.A., Stuart A.C., Fiser A., Sánchez R., Melo F., Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 2000, 29:291-325.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 291-325
-
-
Martí-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sánchez, R.4
Melo, F.5
Sali, A.6
-
5
-
-
70349318376
-
Structure is three to ten times more conserved than sequence - a study of structural response in protein cores
-
Illergård K., Ardell D.H., Elofsson A. Structure is three to ten times more conserved than sequence - a study of structural response in protein cores. Proteins 2009, 77:499-508.
-
(2009)
Proteins
, vol.77
, pp. 499-508
-
-
Illergård, K.1
Ardell, D.H.2
Elofsson, A.3
-
6
-
-
0036304230
-
Protein fold similarity estimated by a probabilistic approach based on Cα-Cα distance comparison
-
Carugo O., Pongor S. Protein fold similarity estimated by a probabilistic approach based on Cα-Cα distance comparison. J. Mol. Biol. 2002, 315:887-898.
-
(2002)
J. Mol. Biol.
, vol.315
, pp. 887-898
-
-
Carugo, O.1
Pongor, S.2
-
8
-
-
0034674175
-
Estimating the number of protein folds and families from complete genome data
-
Wolf Y.I., Grishin N.V., Koonin E.V. Estimating the number of protein folds and families from complete genome data. J. Mol. Biol. 2000, 299:897-905.
-
(2000)
J. Mol. Biol.
, vol.299
, pp. 897-905
-
-
Wolf, Y.I.1
Grishin, N.V.2
Koonin, E.V.3
-
9
-
-
0030870179
-
Relations of the numbers of protein sequences, families and folds
-
Zhang C.T. Relations of the numbers of protein sequences, families and folds. Protein Eng. 1997, 10:757-761.
-
(1997)
Protein Eng.
, vol.10
, pp. 757-761
-
-
Zhang, C.T.1
-
10
-
-
0032545151
-
Estimating the number of protein folds
-
Zhang C., DeLisi C. Estimating the number of protein folds. J. Mol. Biol. 1998, 284:1301-1305.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 1301-1305
-
-
Zhang, C.1
DeLisi, C.2
-
11
-
-
1042302806
-
The number of protein folds and their distribution over families in nature
-
Liu X., Fan K., Wang W. The number of protein folds and their distribution over families in nature. Proteins 2004, 54:491-499.
-
(2004)
Proteins
, vol.54
, pp. 491-499
-
-
Liu, X.1
Fan, K.2
Wang, W.3
-
12
-
-
0028961335
-
SCOP: a structural classification of proteins database for the investigation of sequences and structures
-
Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995, 247:536-540.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
13
-
-
38549153238
-
Data growth and its impact on the SCOP database: new developments
-
Andreeva A., Howorth D., Chandonia J.M., Brenner S.E., Hubbard T.J.P., Chothia C., Murzin G.A. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008, 36:D419-D425.
-
(2008)
Nucleic Acids Res.
, vol.36
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.M.3
Brenner, S.E.4
Hubbard, T.J.P.5
Chothia, C.6
Murzin, G.A.7
-
14
-
-
74249114654
-
Evaluation of template-based models in CASP8 with standard measures
-
Cozzetto D., Kryshtafovych A., Fidelis K., Moult J., Rost B., Tramontano A. Evaluation of template-based models in CASP8 with standard measures. Proteins 2009, 77(Suppl 9):18-28.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 18-28
-
-
Cozzetto, D.1
Kryshtafovych, A.2
Fidelis, K.3
Moult, J.4
Rost, B.5
Tramontano, A.6
-
15
-
-
84858615101
-
Processing and evaluation of predictions in CASP4
-
Moult J., Fidelis K., Zemla A. Processing and evaluation of predictions in CASP4. Proteins 2002, 21:13-21.
-
(2002)
Proteins
, vol.21
, pp. 13-21
-
-
Moult, J.1
Fidelis, K.2
Zemla, A.3
-
16
-
-
0034995092
-
Completeness in structural genomics
-
Vitkup D., Melamud E., Moult J., Sander C. Completeness in structural genomics. Nat. Struct. Biol. 2001, 8:559-566.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 559-566
-
-
Vitkup, D.1
Melamud, E.2
Moult, J.3
Sander, C.4
-
17
-
-
0029907705
-
Modeling of halorhodopsin and rhodopsin based on bacteriorhodopsin
-
Neumüller M., Jähnig F. Modeling of halorhodopsin and rhodopsin based on bacteriorhodopsin. Proteins 1996, 26:146-156.
-
(1996)
Proteins
, vol.26
, pp. 146-156
-
-
Neumüller, M.1
Jähnig, F.2
-
18
-
-
77949360269
-
Template-based protein modeling: recent methodological advances
-
Daga P.R., Patel R.Y., Doerksen R.J. Template-based protein modeling: recent methodological advances. Curr. Top. Med. Chem. 2010, 10:84-94.
-
(2010)
Curr. Top. Med. Chem.
, vol.10
, pp. 84-94
-
-
Daga, P.R.1
Patel, R.Y.2
Doerksen, R.J.3
-
19
-
-
0347899425
-
ArchDB: automated protein loop classification as a tool for structural genomics
-
Espadaler J., Fernandez-Fuentes N., Hermoso A., Querol E., Aviles F.X., Sternberg M.J.E., Oliva B. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res. 2004, 32:D185-D188.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Espadaler, J.1
Fernandez-Fuentes, N.2
Hermoso, A.3
Querol, E.4
Aviles, F.X.5
Sternberg, M.J.E.6
Oliva, B.7
-
20
-
-
34547592557
-
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
-
Davis I.W., Leaver-Fay A., Chen V.B., Block J.N., Kapral G.J., Wang X., et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 2007, 35:W375-W383.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Davis, I.W.1
Leaver-Fay, A.2
Chen, V.B.3
Block, J.N.4
Kapral, G.J.5
Wang, X.6
-
21
-
-
0000243829
-
PROCHECK: a program to check the stereochemical quality of protein structures
-
Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 1993, 26:283-291.
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
22
-
-
0030047142
-
Errors in protein structures
-
Hooft R.W., Vriend G., Sander C., Abola E.E. Errors in protein structures. Nature 1996, 381:272.
-
(1996)
Nature
, vol.381
, pp. 272
-
-
Hooft, R.W.1
Vriend, G.2
Sander, C.3
Abola, E.E.4
-
23
-
-
33745714411
-
On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins
-
Forrest L.R., Tang C.L., Honig B. On the accuracy of homology modeling and sequence alignment methods applied to membrane proteins. Biophys. J. 2006, 91:508-517.
-
(2006)
Biophys. J.
, vol.91
, pp. 508-517
-
-
Forrest, L.R.1
Tang, C.L.2
Honig, B.3
-
24
-
-
77958567426
-
Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening
-
Brylinski M., Skolnick J. Comprehensive structural and functional characterization of the human kinome by protein structure modeling and ligand virtual screening. J. Chem. Inf. Model. 2010, 50:1839-1854.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1839-1854
-
-
Brylinski, M.1
Skolnick, J.2
-
25
-
-
66349085848
-
Identification of a novel inhibitor of JAK2 tyrosine kinase by structure-based virtual screening
-
Kiss R., Polgár T., Kirabo A., Sayyah J., Figueroa N.C., List A.F., Sokol L., Zuckerman K.S., Gali M., Bisht K.S., Sayeski P.P., Keseru G.M. Identification of a novel inhibitor of JAK2 tyrosine kinase by structure-based virtual screening. Bioorg. Med. Chem. Lett. 2009, 19:3598-3601.
-
(2009)
Bioorg. Med. Chem. Lett.
, vol.19
, pp. 3598-3601
-
-
Kiss, R.1
Polgár, T.2
Kirabo, A.3
Sayyah, J.4
Figueroa, N.C.5
List, A.F.6
Sokol, L.7
Zuckerman, K.S.8
Gali, M.9
Bisht, K.S.10
Sayeski, P.P.11
Keseru, G.M.12
-
26
-
-
33746049159
-
Homology model of RSK2 N-terminal kinase domain, structure-based identification of novel RSK2 inhibitors, and preliminary common pharmacophore
-
Nguyen T.L., Gussio R., Smith J.A., Lannigan D.A., Hecht S.M., Scudiero D.A., Shoemaker R.H., Zaharevitz D.W. Homology model of RSK2 N-terminal kinase domain, structure-based identification of novel RSK2 inhibitors, and preliminary common pharmacophore. Bioorg. Med. Chem. 2006, 14:6097-6105.
-
(2006)
Bioorg. Med. Chem.
, vol.14
, pp. 6097-6105
-
-
Nguyen, T.L.1
Gussio, R.2
Smith, J.A.3
Lannigan, D.A.4
Hecht, S.M.5
Scudiero, D.A.6
Shoemaker, R.H.7
Zaharevitz, D.W.8
-
27
-
-
39149107126
-
Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening
-
Cavasotto C.N., Orry A.J.W., Murgolo N.J., Czarniecki M.F., Kocsi S.A., Hawes B.E., O'Neill K.A., Hine H., Burton M.S., Voigt J.H., Abagyan R.A., Bayne M.L., Monsma F.J. Discovery of novel chemotypes to a G-protein-coupled receptor through ligand-steered homology modeling and structure-based virtual screening. J. Med. Chem. 2008, 51:581-588.
-
(2008)
J. Med. Chem.
, vol.51
, pp. 581-588
-
-
Cavasotto, C.N.1
Orry, A.J.W.2
Murgolo, N.J.3
Czarniecki, M.F.4
Kocsi, S.A.5
Hawes, B.E.6
O'Neill, K.A.7
Hine, H.8
Burton, M.S.9
Voigt, J.H.10
Abagyan, R.A.11
Bayne, M.L.12
Monsma, F.J.13
-
28
-
-
42149139028
-
A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists
-
Engel S., Skoumbourdis A.P., Childress J., Neumann S., Deschamps J.R., Thomas C.J., Colson A.O., Constanzi S., Gershengorn M.C. A virtual screen for diverse ligands: discovery of selective G protein-coupled receptor antagonists. J. Am. Chem. Soc. 2008, 130:5115-5123.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 5115-5123
-
-
Engel, S.1
Skoumbourdis, A.P.2
Childress, J.3
Neumann, S.4
Deschamps, J.R.5
Thomas, C.J.6
Colson, A.O.7
Constanzi, S.8
Gershengorn, M.C.9
-
29
-
-
44949168495
-
Discovery of novel human histamine H4 receptor ligands by large-scale structure-based virtual screening
-
Kiss R., Kiss B., Könczöl Á., Szalai F., Jelinek I., László V., Noszál B., Falus A., Keseru G.M. Discovery of novel human histamine H4 receptor ligands by large-scale structure-based virtual screening. J. Med. Chem. 2008, 51:3145-3153.
-
(2008)
J. Med. Chem.
, vol.51
, pp. 3145-3153
-
-
Kiss, R.1
Kiss, B.2
Könczöl, Á.3
Szalai, F.4
Jelinek, I.5
László, V.6
Noszál, B.7
Falus, A.8
Keseru, G.M.9
-
30
-
-
45749109114
-
Homology model-based virtual screening for GPCR ligands using docking and target-biased scoring
-
Radestock S., Weil T., Renner S. Homology model-based virtual screening for GPCR ligands using docking and target-biased scoring. J. Chem. Inf. Model. 2008, 48:1104-1117.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1104-1117
-
-
Radestock, S.1
Weil, T.2
Renner, S.3
-
31
-
-
77449138099
-
Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: application to H3 antagonists
-
Rai B.K., Tawa G.J., Katz A.H., Humblet C. Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: application to H3 antagonists. Proteins 2010, 78:457-473.
-
(2010)
Proteins
, vol.78
, pp. 457-473
-
-
Rai, B.K.1
Tawa, G.J.2
Katz, A.H.3
Humblet, C.4
-
32
-
-
77957839624
-
Novel structural insights for drug design of selective 5-HT(2C) inverse agonists from a ligand-biased receptor model
-
Renault N., Gohier A., Chavatte P., Farce A. Novel structural insights for drug design of selective 5-HT(2C) inverse agonists from a ligand-biased receptor model. Eur. J. Med. Chem. 2010, 45:5086-5099.
-
(2010)
Eur. J. Med. Chem.
, vol.45
, pp. 5086-5099
-
-
Renault, N.1
Gohier, A.2
Chavatte, P.3
Farce, A.4
-
33
-
-
38949186792
-
Virtual screening approaches for the identification of non-lipid autotaxin inhibitors
-
Parrill A.L., Echols U., Nguyen T., Pham T.C.T., Hoeglund A., Baker D.L. Virtual screening approaches for the identification of non-lipid autotaxin inhibitors. Bioorg. Med. Chem. 2008, 16:1784-1795.
-
(2008)
Bioorg. Med. Chem.
, vol.16
, pp. 1784-1795
-
-
Parrill, A.L.1
Echols, U.2
Nguyen, T.3
Pham, T.C.T.4
Hoeglund, A.5
Baker, D.L.6
-
34
-
-
45749158183
-
Probing the structures of leishmanial farnesyl pyrophosphate synthases: homology modeling and docking studies
-
Mukherjee P., Desai P.V., Srivastava A., Tekwani B.L., Avery M.A. Probing the structures of leishmanial farnesyl pyrophosphate synthases: homology modeling and docking studies. J. Chem. Inf. Model. 2008, 48:1026-1040.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1026-1040
-
-
Mukherjee, P.1
Desai, P.V.2
Srivastava, A.3
Tekwani, B.L.4
Avery, M.A.5
-
35
-
-
84855685438
-
Homology modeling and in silico screening of inhibitors for the substrate binding domain of human Siah2: implications for hypoxia-induced cancers
-
Anupriya G., Roopa K., Basappa S., Chong Y.S., Annamalai L. Homology modeling and in silico screening of inhibitors for the substrate binding domain of human Siah2: implications for hypoxia-induced cancers. J. Mol. Model. 2011, 17:3325-3332.
-
(2011)
J. Mol. Model.
, vol.17
, pp. 3325-3332
-
-
Anupriya, G.1
Roopa, K.2
Basappa, S.3
Chong, Y.S.4
Annamalai, L.5
-
36
-
-
55249114698
-
Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening
-
Kalyanaraman C., Imker H.J., Fedorov A.A., Fedorov E.V., Glasner M.E., Babbitt P.C., Almo S.C., Gerlt J.A., Jacobson M.P. Discovery of a dipeptide epimerase enzymatic function guided by homology modeling and virtual screening. Structure 2008, 16:1668-1677.
-
(2008)
Structure
, vol.16
, pp. 1668-1677
-
-
Kalyanaraman, C.1
Imker, H.J.2
Fedorov, A.A.3
Fedorov, E.V.4
Glasner, M.E.5
Babbitt, P.C.6
Almo, S.C.7
Gerlt, J.A.8
Jacobson, M.P.9
-
37
-
-
0021919480
-
Rapid and sensitive protein similarity searches
-
Lipman D., Pearson W. Rapid and sensitive protein similarity searches. Science 1985, 227:1435-1441.
-
(1985)
Science
, vol.227
, pp. 1435-1441
-
-
Lipman, D.1
Pearson, W.2
-
39
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25:3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schäffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.7
-
40
-
-
23144452044
-
The HHpred interactive server for protein homology detection and structure prediction
-
Söding J., Biegert A., Lupas A.N. The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 2005, 33:W244-W248.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Söding, J.1
Biegert, A.2
Lupas, A.N.3
-
41
-
-
63849246525
-
Protein structure prediction on the Web: a case study using the Phyre server
-
Kelley L.A., Sternberg M.J.E. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4:363-371.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 363-371
-
-
Kelley, L.A.1
Sternberg, M.J.E.2
-
42
-
-
4444298729
-
Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods
-
Ohlson T., Wallner B., Elofsson A. Profile-profile methods provide improved fold-recognition: a study of different profile-profile alignment methods. Proteins 2004, 57:188-197.
-
(2004)
Proteins
, vol.57
, pp. 188-197
-
-
Ohlson, T.1
Wallner, B.2
Elofsson, A.3
-
43
-
-
2442663920
-
Scoring profile-to-profile sequence alignments
-
Wang G., Dunbrack R.L. Scoring profile-to-profile sequence alignments. Protein Sci. 2004, 13:1612-1626.
-
(2004)
Protein Sci.
, vol.13
, pp. 1612-1626
-
-
Wang, G.1
Dunbrack, R.L.2
-
44
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005, 21:951-960.
-
(2005)
Bioinformatics
, vol.21
, pp. 951-960
-
-
Söding, J.1
-
45
-
-
0032962457
-
Twilight zone of protein sequence alignments
-
Rost B. Twilight zone of protein sequence alignments. Protein Eng. 1999, 12:85-94.
-
(1999)
Protein Eng.
, vol.12
, pp. 85-94
-
-
Rost, B.1
-
47
-
-
35748965848
-
Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments
-
Fernandez-Fuentes N., Rai B.K., Madrid-Aliste C.J., Fajardo J.E., Fiser A. Comparative protein structure modeling by combining multiple templates and optimizing sequence-to-structure alignments. Bioinformatics 2007, 23:2558-2565.
-
(2007)
Bioinformatics
, vol.23
, pp. 2558-2565
-
-
Fernandez-Fuentes, N.1
Rai, B.K.2
Madrid-Aliste, C.J.3
Fajardo, J.E.4
Fiser, A.5
-
48
-
-
44349091007
-
Using multiple templates to improve quality of homology models in automated homology modeling
-
Wallner R.N., Lindahl E., Elofsson A. Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci. 2008, 990-1002.
-
(2008)
Protein Sci.
, pp. 990-1002
-
-
Wallner, R.N.1
Lindahl, E.2
Elofsson, A.3
-
49
-
-
34548136236
-
An evaluation of automated homology modelling methods at low target template sequence similarity
-
Dalton J.A.R., Jackson R.M. An evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics 2007, 23:1901-1908.
-
(2007)
Bioinformatics
, vol.23
, pp. 1901-1908
-
-
Dalton, J.A.R.1
Jackson, R.M.2
-
50
-
-
36448991500
-
Clustal W and Clustal X version 2.0
-
Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
-
(2007)
Bioinformatics
, vol.23
, pp. 2947-2948
-
-
Larkin, M.A.1
Blackshields, G.2
Brown, N.P.3
Chenna, R.4
McGettigan, P.A.5
McWilliam, H.6
Valentin, F.7
Wallace, I.M.8
Wilm, A.9
Lopez, R.10
Thompson, J.D.11
Gibson, T.J.12
Higgins, D.G.13
-
51
-
-
0034623005
-
T-Coffee: a novel method for fast and accurate multiple sequence alignment
-
Notredame C., Higgins D.G., Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000, 302:205-217.
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 205-217
-
-
Notredame, C.1
Higgins, D.G.2
Heringa, J.3
-
52
-
-
2942619012
-
3DCoffee: combining protein sequences and structures within multiple sequence alignments
-
O'Sullivan O., Suhre K., Abergel C., Higgins D.G., Notredame C. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J. Mol. Biol. 2004, 340:385-395.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 385-395
-
-
O'Sullivan, O.1
Suhre, K.2
Abergel, C.3
Higgins, D.G.4
Notredame, C.5
-
53
-
-
3042666256
-
MUSCLE: multiple sequence alignment with high accuracy and high throughput
-
Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1792-1797
-
-
Edgar, R.C.1
-
54
-
-
36749103110
-
Automated server predictions in CASP7
-
Battey J.N.D., Kopp J., Bordoli L., Read R.J., Clarke N.D., Schwede T. Automated server predictions in CASP7. Proteins 2007, 69(Suppl 8):68-82.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 68-82
-
-
Battey, J.N.D.1
Kopp, J.2
Bordoli, L.3
Read, R.J.4
Clarke, N.D.5
Schwede, T.6
-
55
-
-
74249106219
-
I-TASSER: fully automated protein structure prediction in CASP8
-
Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins 2009, 77(Suppl 9):100-113.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 100-113
-
-
Zhang, Y.1
-
56
-
-
33745076219
-
Advances in homology protein structure modeling
-
Xiang Z. Advances in homology protein structure modeling. Curr. Protein Pept. Sci. 2006, 7:217-227.
-
(2006)
Curr. Protein Pept. Sci.
, vol.7
, pp. 217-227
-
-
Xiang, Z.1
-
57
-
-
0035747672
-
Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM
-
Bates P.A., Kelley L.A., MacCallum R.M., Sternberg M.J.E. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins. Suppl 2002, 5:39-46.
-
(2002)
Proteins. Suppl
, vol.5
, pp. 39-46
-
-
Bates, P.A.1
Kelley, L.A.2
MacCallum, R.M.3
Sternberg, M.J.E.4
-
58
-
-
0029565303
-
A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling
-
Koehl P., Delarue M. A self consistent mean field approach to simultaneous gap closure and side-chain positioning in homology modelling. Nat. Struct. Biol. 1995, 2:163-170.
-
(1995)
Nat. Struct. Biol.
, vol.2
, pp. 163-170
-
-
Koehl, P.1
Delarue, M.2
-
59
-
-
32144432437
-
The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
-
Arnold K., Bordoli L., Kopp J., Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22:195-201.
-
(2006)
Bioinformatics
, vol.22
, pp. 195-201
-
-
Arnold, K.1
Bordoli, L.2
Kopp, J.3
Schwede, T.4
-
60
-
-
0026754015
-
Accurate modeling of protein conformation by automatic segment matching
-
Levitt M. Accurate modeling of protein conformation by automatic segment matching. J. Mol. Biol. 1992, 226:507-533.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 507-533
-
-
Levitt, M.1
-
61
-
-
43749107283
-
Comparative protein structure modeling using MODELLER
-
Eswar N., Webb B., Marti-Renom M.A., Madhusudhan M.S., Eramian D., Shen M.-Y., et al. Comparative protein structure modeling using MODELLER. Curr. Protoc. Bioinformatics 2006, (Suppl. 15):5.6.1-5.6.30.
-
(2006)
Curr. Protoc. Bioinformatics
, Issue.SUPPL. 15
-
-
Eswar, N.1
Webb, B.2
Marti-Renom, M.A.3
Madhusudhan, M.S.4
Eramian, D.5
Shen, M.-Y.6
-
62
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
Sali A., Blundell T. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234:779-815.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 779-815
-
-
Sali, A.1
Blundell, T.2
-
63
-
-
10744220076
-
Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling
-
Petrey D., Xiang Z., Tang C.L., Xie L., Gimpelev M., Mitros T., Soto C.S., Goldsmith-Fischman S., Kernytsky A., Schlessinger A., Koh I.Y.Y., Alexov E., Honig B. Using multiple structure alignments, fast model building, and energetic analysis in fold recognition and homology modeling. Proteins 2003, 53(Suppl 6):430-435.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 430-435
-
-
Petrey, D.1
Xiang, Z.2
Tang, C.L.3
Xie, L.4
Gimpelev, M.5
Mitros, T.6
Soto, C.S.7
Goldsmith-Fischman, S.8
Kernytsky, A.9
Schlessinger, A.10
Koh, I.Y.Y.11
Alexov, E.12
Honig, B.13
-
64
-
-
17744387920
-
All are not equal: a benchmark of different homology modeling programs
-
Wallner B., Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Sci. 2005, 14:1315-1327.
-
(2005)
Protein Sci.
, vol.14
, pp. 1315-1327
-
-
Wallner, B.1
Elofsson, A.2
-
65
-
-
74249121740
-
Assessment of the protein-structure refinement category in CASP8
-
MacCallum J.L., Hua L., Schnieders M.J., Pande V.S., Jacobson M.P., Dill K.a Assessment of the protein-structure refinement category in CASP8. Proteins 2009, 77(Suppl 9):66-80.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 66-80
-
-
MacCallum, J.L.1
Hua, L.2
Schnieders, M.J.3
Pande, V.S.4
Jacobson, M.P.5
Dill, K.A.6
-
66
-
-
70450106216
-
Improved prediction of protein side-chain conformations with SCWRL4
-
Krivov G.G., Shapovalov M.V., Dunbrack R.L. Improved prediction of protein side-chain conformations with SCWRL4. Proteins 2009, 77:778-795.
-
(2009)
Proteins
, vol.77
, pp. 778-795
-
-
Krivov, G.G.1
Shapovalov, M.V.2
Dunbrack, R.L.3
-
68
-
-
0035107308
-
CODA: a combined algorithm for predicting the structurally variable regions of protein models
-
Deane C.M., Blundell T.L. CODA: a combined algorithm for predicting the structurally variable regions of protein models. Protein Sci. 2001, 10:599-612.
-
(2001)
Protein Sci.
, vol.10
, pp. 599-612
-
-
Deane, C.M.1
Blundell, T.L.2
-
69
-
-
1642464839
-
Protein structure prediction using Rosetta
-
Rohl C.A., Strauss C.E., Misura K.M., Baker D. Protein structure prediction using Rosetta. Meth. Enzymol. 2004, 383:66-93.
-
(2004)
Meth. Enzymol.
, vol.383
, pp. 66-93
-
-
Rohl, C.A.1
Strauss, C.E.2
Misura, K.M.3
Baker, D.4
-
70
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
Sippl M.J. Recognition of errors in three-dimensional structures of proteins. Proteins 1993, 17:355-362.
-
(1993)
Proteins
, vol.17
, pp. 355-362
-
-
Sippl, M.J.1
-
71
-
-
34547566446
-
ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
-
Wiederstein M., Sippl M.J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res. 2007, 35:W407-W410.
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Wiederstein, M.1
Sippl, M.J.2
-
72
-
-
0026610767
-
Assessment of protein models with three-dimensional profiles
-
Lüthy R., Bowie J.U., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 1992, 356:83-85.
-
(1992)
Nature
, vol.356
, pp. 83-85
-
-
Lüthy, R.1
Bowie, J.U.2
Eisenberg, D.3
-
73
-
-
0025830469
-
A method to identify protein sequences that fold into a known three-dimensional structure
-
Bowie J.U., Lüthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253:164-170.
-
(1991)
Science
, vol.253
, pp. 164-170
-
-
Bowie, J.U.1
Lüthy, R.2
Eisenberg, D.3
-
74
-
-
0022706389
-
The relation between the divergence of sequence and structure in proteins
-
Chothia C., Lesk A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986, 5:823-826.
-
(1986)
EMBO J.
, vol.5
, pp. 823-826
-
-
Chothia, C.1
Lesk, A.M.2
-
75
-
-
77954065271
-
I-TASSER: a unified platform for automated protein structure and function prediction
-
Roy A., Kucukural A., Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 2010, 5:725-738.
-
(2010)
Nat. Protoc.
, vol.5
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
76
-
-
34250851687
-
LOMETS: a local meta-threading-server for protein structure prediction
-
Wu S., Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res. 2007, 35:3375-3382.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 3375-3382
-
-
Wu, S.1
Zhang, Y.2
-
77
-
-
23044531267
-
Protein recognition by sequence-to-structure fitness: bridging efficiency and capacity of threading models
-
John Wiley & Sons, Inc., New York, R.A. Friesner, I. Prigogine, S.A. Rice (Eds.)
-
Meller J., Elber R. Protein recognition by sequence-to-structure fitness: bridging efficiency and capacity of threading models. Computational Methods for Protein Folding 2002, 77-130. John Wiley & Sons, Inc., New York. R.A. Friesner, I. Prigogine, S.A. Rice (Eds.).
-
(2002)
Computational Methods for Protein Folding
, pp. 77-130
-
-
Meller, J.1
Elber, R.2
-
78
-
-
37149010716
-
Protein structure prediction using threading
-
Xu J., Jiao F., Yu L. Protein structure prediction using threading. Methods Mol. Biol. 2008, 413:91-121.
-
(2008)
Methods Mol. Biol.
, vol.413
, pp. 91-121
-
-
Xu, J.1
Jiao, F.2
Yu, L.3
-
79
-
-
0026690571
-
A new approach to protein fold recognition
-
Jones D.T., Taylor W.R., Thornton J.M. A new approach to protein fold recognition. Nature 1992, 358:86-89.
-
(1992)
Nature
, vol.358
, pp. 86-89
-
-
Jones, D.T.1
Taylor, W.R.2
Thornton, J.M.3
-
80
-
-
0030052366
-
Protein fold recognition by sequence threading: tools and assessment techniques
-
Miller R.T., Jones D.T., Thornton J.M. Protein fold recognition by sequence threading: tools and assessment techniques. FASEB J. 1996, 10:171-178.
-
(1996)
FASEB J.
, vol.10
, pp. 171-178
-
-
Miller, R.T.1
Jones, D.T.2
Thornton, J.M.3
-
81
-
-
0242369082
-
RAPTOR: optimal protein threading by linear programming
-
Xu J., Li M., Kim D., Xu Y. RAPTOR: optimal protein threading by linear programming. J. Bioinform. Comput. Biol. 2003, 1:95-117.
-
(2003)
J. Bioinform. Comput. Biol.
, vol.1
, pp. 95-117
-
-
Xu, J.1
Li, M.2
Kim, D.3
Xu, Y.4
-
82
-
-
0024733407
-
Intermediates and barrier crossing in a random energy model (with applications to protein folding)
-
Bryngelson J.D., Wolynes P.G. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J. Phys. Chem. 1989, 93:6902-6915.
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 6902-6915
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
83
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill K.A., Chan H.S. From Levinthal to pathways to funnels. Nat. Struct. Biol. 1997, 4:10-19.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
84
-
-
0033545962
-
Protein structure prediction by global optimization of a potential energy function
-
Liwo A., Lee J., Ripoll D.R., Pillardy J., Scheraga H.A. Protein structure prediction by global optimization of a potential energy function. Proc. Natl. Acad. Sci. U.S.A. 1999, 96:5482-5485.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A.
, vol.96
, pp. 5482-5485
-
-
Liwo, A.1
Lee, J.2
Ripoll, D.R.3
Pillardy, J.4
Scheraga, H.A.5
-
85
-
-
21144442648
-
Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests
-
Ołdziej S., Czaplewski C., Liwo A., Chinchio M., Nanias M., Vila J.A., Khalili M., Arnautova Y.A., Jagielska A., Makowski M., Schafroth H.D., Kaźmierkiewicz R., Ripoll D.R., Pillardy J., Saunders J.A., Kang Y.K., Gibson K.D., Scheraga H.A. Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:7547-7552.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 7547-7552
-
-
Ołdziej, S.1
Czaplewski, C.2
Liwo, A.3
Chinchio, M.4
Nanias, M.5
Vila, J.A.6
Khalili, M.7
Arnautova, Y.A.8
Jagielska, A.9
Makowski, M.10
Schafroth, H.D.11
Kaźmierkiewicz, R.12
Ripoll, D.R.13
Pillardy, J.14
Saunders, J.A.15
Kang, Y.K.16
Gibson, K.D.17
Scheraga, H.A.18
-
86
-
-
12944263648
-
Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study
-
Klepeis J.L., Wei Y., Hecht M.H., Floudas C.A. Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins 2005, 58:560-570.
-
(2005)
Proteins
, vol.58
, pp. 560-570
-
-
Klepeis, J.L.1
Wei, Y.2
Hecht, M.H.3
Floudas, C.A.4
-
87
-
-
0141642142
-
ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence
-
Klepeis J.L., Floudas C.A. ASTRO-FOLD: a combinatorial and global optimization framework for ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys. J. 2003, 85:2119-2146.
-
(2003)
Biophys. J.
, vol.85
, pp. 2119-2146
-
-
Klepeis, J.L.1
Floudas, C.A.2
-
88
-
-
34249869832
-
Ab initio modeling of small proteins by iterative TASSER simulations
-
Wu S., Skolnick J., Zhang Y. Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol. 2007, 5.
-
(2007)
BMC Biol.
, vol.5
-
-
Wu, S.1
Skolnick, J.2
Zhang, Y.3
-
89
-
-
39449115394
-
I-TASSER server for protein 3D structure prediction
-
Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9:40.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 40
-
-
Zhang, Y.1
-
90
-
-
50649095790
-
Macromolecular modeling with Rosetta
-
Das R., Baker D. Macromolecular modeling with Rosetta. Annu. Rev. Biochem. 2008, 77:363-382.
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 363-382
-
-
Das, R.1
Baker, D.2
-
91
-
-
0032929780
-
Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
-
Simons K.T., Ruczinski I., Kooperberg C., Fox B.A., Bystroff C., Baker D. Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 1999, 34:82-95.
-
(1999)
Proteins
, vol.34
, pp. 82-95
-
-
Simons, K.T.1
Ruczinski, I.2
Kooperberg, C.3
Fox, B.A.4
Bystroff, C.5
Baker, D.6
-
92
-
-
0041843696
-
TOUCHSTONE II: a new approach to ab initio protein structure prediction
-
Zhang Y., Kolinski A., Skolnick J. TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys. J. 2003, 85:1145-1164.
-
(2003)
Biophys. J.
, vol.85
, pp. 1145-1164
-
-
Zhang, Y.1
Kolinski, A.2
Skolnick, J.3
-
93
-
-
0036681386
-
Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding
-
Zhang Y., Kihara D., Skolnick J. Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 2002, 48:192-201.
-
(2002)
Proteins
, vol.48
, pp. 192-201
-
-
Zhang, Y.1
Kihara, D.2
Skolnick, J.3
-
94
-
-
41349114023
-
A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
-
Wu S., Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 2008, 24:924-931.
-
(2008)
Bioinformatics
, vol.24
, pp. 924-931
-
-
Wu, S.1
Zhang, Y.2
-
95
-
-
1942519275
-
SPICKER: a clustering approach to identify near-native protein folds
-
Zhang Y., Skolnick J. SPICKER: a clustering approach to identify near-native protein folds. J. Comput. Chem. 2004, 25:865-871.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 865-871
-
-
Zhang, Y.1
Skolnick, J.2
-
96
-
-
17644392830
-
TM-align: a protein structure alignment algorithm based on the TM-score
-
Zhang Y., Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005, 33:2302-2309.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2302-2309
-
-
Zhang, Y.1
Skolnick, J.2
-
97
-
-
68049138029
-
REMO: a new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks
-
Li Y., Zhang Y. REMO: a new protocol to refine full atomic protein models from C-alpha traces by optimizing hydrogen-bonding networks. Proteins 2009, 76:665-676.
-
(2009)
Proteins
, vol.76
, pp. 665-676
-
-
Li, Y.1
Zhang, Y.2
-
98
-
-
77951941264
-
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8
-
Wang Z., Eickholt J., Cheng J. MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8. Bioinformatics 2010, 26:882-888.
-
(2010)
Bioinformatics
, vol.26
, pp. 882-888
-
-
Wang, Z.1
Eickholt, J.2
Cheng, J.3
-
99
-
-
77951234057
-
MUFOLD: a new solution for protein 3D structure prediction
-
Zhang J., Wang Q., Barz B., He Z., Kosztin I., Shang Y., Xu D. MUFOLD: a new solution for protein 3D structure prediction. Proteins 2010, 78:1137-1152.
-
(2010)
Proteins
, vol.78
, pp. 1137-1152
-
-
Zhang, J.1
Wang, Q.2
Barz, B.3
He, Z.4
Kosztin, I.5
Shang, Y.6
Xu, D.7
-
100
-
-
64549115839
-
Protein structure prediction: when is it useful?
-
Zhang Y. Protein structure prediction: when is it useful?. Curr. Opin. Struct. Biol. 2009, 19:145-155.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 145-155
-
-
Zhang, Y.1
-
101
-
-
34247362408
-
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology
-
Malmström L., Riffle M., Strauss C.E.M., Chivian D., Davis T.N., Bonneau R., Baker D. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol. 2007, 5:e76.
-
(2007)
PLoS Biol.
, vol.5
-
-
Malmström, L.1
Riffle, M.2
Strauss, C.E.M.3
Chivian, D.4
Davis, T.N.5
Bonneau, R.6
Baker, D.7
-
102
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
Harris, M.A.11
Hill, D.P.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.C.16
Richardson, J.E.17
Ringwald, M.18
Rubin, G.M.19
Sherlock, G.20
more..
-
103
-
-
74249107702
-
Assessment of CASP8 structure predictions for template free targets
-
Ben-David M., Noivirt-Brik O., Paz A., Prilusky J., Sussman J.L., Levy Y. Assessment of CASP8 structure predictions for template free targets. Proteins 2009, 77(Suppl 9):50-65.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 50-65
-
-
Ben-David, M.1
Noivirt-Brik, O.2
Paz, A.3
Prilusky, J.4
Sussman, J.L.5
Levy, Y.6
-
104
-
-
0242443693
-
Force fields for protein simulations
-
Ponder J.W., Case D.A. Force fields for protein simulations. Adv. Protein Chem. 2003, 66:27-85.
-
(2003)
Adv. Protein Chem.
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
105
-
-
67650500988
-
CHARMM: the biomolecular simulation program
-
Brooks B.R., Brooks C.L., Mackerell A.D., Nilsson L., Petrella R.J., Roux B., Won Y., Archontis G., Bartels C., Boresch S., Caflisch A., Caves L., Cui Q., Dinner A.R., Feig M., Fischer S., Gao J., Hodoscek M., Im W., Kuczera K,., Lazaridis T., Ma J., Ovchinnikov V., Paci E., Pastor R.W., Post C.B., Pu J.Z., Schaeffer M., Tidor B., Venable R.M., Woodcock H.L., Wu X., Yang W., York D.M., Karplus M. CHARMM: the biomolecular simulation program. J. Comput. Chem. 2009, 30:1545-1614.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks, C.L.2
Mackerell, A.D.3
Nilsson, L.4
Petrella, R.J.5
Roux, B.6
Won, Y.7
Archontis, G.8
Bartels, C.9
Boresch, S.10
Caflisch, A.11
Caves, L.12
Cui, Q.13
Dinner, A.R.14
Feig, M.15
Fischer, S.16
Gao, J.17
Hodoscek, M.18
Im, W.19
Kuczera, K.20
Lazaridis, T.21
Ma, J.22
Ovchinnikov, V.23
Paci, E.24
Pastor, R.W.25
Post, C.B.26
Pu, J.Z.27
Schaeffer, M.28
Tidor, B.29
Venable, R.M.30
Woodcock, H.L.31
Wu, X.32
Yang, W.33
York, D.M.34
Karplus, M.35
more..
-
106
-
-
84986512474
-
CHARMM: a program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson D.J., States D.J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 1983, 4:187-217.
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, D.J.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
107
-
-
0000224283
-
-
The Encyclopedia of Computational Chemistry, John Wiley & Sons, Chichester, P. Schleyer (Ed.)
-
MacKerel A.D., Brooks C.L., Nilsson L., Roux B., Won Y., Karplus M. CHARMM: The Energy Function and Its Parameterization with an Overview of the Program 1998, 271-277. The Encyclopedia of Computational Chemistry, John Wiley & Sons, Chichester, Vol. 1. P. Schleyer (Ed.).
-
(1998)
CHARMM: The Energy Function and Its Parameterization with an Overview of the Program
, vol.1
, pp. 271-277
-
-
MacKerel, A.D.1
Brooks, C.L.2
Nilsson, L.3
Roux, B.4
Won, Y.5
Karplus, M.6
-
108
-
-
23444454552
-
The Amber biomolecular simulation programs
-
Case D.A., Cheatham T.E., Darden T., Gohlke H., Luo R., Merz K.M., Onufriev A., Simmerling C., Wang B., Woods R.J. The Amber biomolecular simulation programs. Comput. Chem. 2005, 26:1668-1688.
-
(2005)
Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
109
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen W.L., Maxwell D.S., Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 1996, 118:11225-11236.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
110
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski G.A., Friesner R.A., Tirado-Rives J., Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 2001, 105:6474-6487.
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
111
-
-
30444448249
-
The GROMOS software for biomolecular simulation: GROMOS05
-
Christen M., Hünenberger P.H., Bakowies D., Baron R., Bürgi R., Geerke D.P., et al. The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 2005, 26:1719-1751.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1719-1751
-
-
Christen, M.1
Hünenberger, P.H.2
Bakowies, D.3
Baron, R.4
Bürgi, R.5
Geerke, D.P.6
-
112
-
-
84934440741
-
Comparison of protein force fields for molecular dynamics simulations
-
Guvench O., MacKerell A.D. Comparison of protein force fields for molecular dynamics simulations. Methods Mol. Biol. 2008, 443:63-88.
-
(2008)
Methods Mol. Biol.
, vol.443
, pp. 63-88
-
-
Guvench, O.1
MacKerell, A.D.2
-
113
-
-
34548717559
-
Phase transition for a hard sphere system
-
Alder B.J., Wainwright T.E. Phase transition for a hard sphere system. J. Chem. Phys. 1957, 27:1208-1209.
-
(1957)
J. Chem. Phys.
, vol.27
, pp. 1208-1209
-
-
Alder, B.J.1
Wainwright, T.E.2
-
114
-
-
36849126204
-
Studies in molecular dynamics. I. General method
-
Alder B.J., Wainwright T.E. Studies in molecular dynamics. I. General method. J. Chem. Phys. 1959, 31:459-466.
-
(1959)
J. Chem. Phys.
, vol.31
, pp. 459-466
-
-
Alder, B.J.1
Wainwright, T.E.2
-
115
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips J.C., Braun R., Wang W., Gumbart J., Tajkhorshid E., Villa E., Chipot C., Skeel R.D., Kalé L., Schulten K. Scalable molecular dynamics with NAMD. J. Comput. Chem. 2005, 26:1781-1802.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kalé, L.9
Schulten, K.10
-
116
-
-
46249092554
-
GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess B., Kutzner C., van der Spoel D., Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory. Comput. 2008, 4:435-447.
-
(2008)
J. Chem. Theory. Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
117
-
-
27344454932
-
GROMACS: fast, flexible, and free
-
van der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J.C. GROMACS: fast, flexible, and free. J. Comput. Chem. 2005, 26:1701-1718.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
van der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
119
-
-
0028020035
-
Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer
-
Woolf T.B., Roux B. Molecular dynamics simulation of the gramicidin channel in a phospholipid bilayer. Proc. Natl. Acad. Sci. U.S.A. 1994, 91:11631-11635.
-
(1994)
Proc. Natl. Acad. Sci. U.S.A.
, vol.91
, pp. 11631-11635
-
-
Woolf, T.B.1
Roux, B.2
-
120
-
-
0029026347
-
Structure and fluctuations of bacteriorhodopsin in the purple membrane: a molecular dynamics study
-
Edholm O., Berger O., Jähnig F. Structure and fluctuations of bacteriorhodopsin in the purple membrane: a molecular dynamics study. J. Mol. Biol. 1995, 250:94-111.
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 94-111
-
-
Edholm, O.1
Berger, O.2
Jähnig, F.3
-
122
-
-
77954757239
-
Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1
-
Dolenc J., Missimer J.H., Steinmetz M.O., van Gunsteren W.F. Methods of NMR structure refinement: molecular dynamics simulations improve the agreement with measured NMR data of a C-terminal peptide of GCN4-p1. J. Biomol. NMR 2010, 47:221-235.
-
(2010)
J. Biomol. NMR
, vol.47
, pp. 221-235
-
-
Dolenc, J.1
Missimer, J.H.2
Steinmetz, M.O.3
van Gunsteren, W.F.4
-
123
-
-
77957963878
-
Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations
-
Subbotina J., Yarov-Yarovoy V., Lees-Miller J., Durdagi S., Guo J., Duff H.J., Noskov Y.S. Structural refinement of the hERG1 pore and voltage-sensing domains with ROSETTA-membrane and molecular dynamics simulations. Proteins 2010, 78:2922-2934.
-
(2010)
Proteins
, vol.78
, pp. 2922-2934
-
-
Subbotina, J.1
Yarov-Yarovoy, V.2
Lees-Miller, J.3
Durdagi, S.4
Guo, J.5
Duff, H.J.6
Noskov, Y.S.7
-
124
-
-
67849090867
-
Binding and enantiomeric selectivity of threonyl-tRNA synthetase
-
Malde A.K., Mark A.E. Binding and enantiomeric selectivity of threonyl-tRNA synthetase. J. Am. Chem. Soc. 2009, 131:3848-3849.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 3848-3849
-
-
Malde, A.K.1
Mark, A.E.2
-
125
-
-
76649136949
-
Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors
-
Durrant J.D., de Oliveira C.A.F., McCammon J.A. Including receptor flexibility and induced fit effects into the design of MMP-2 inhibitors. J. Mol. Recognit. 2010, 23:173-182.
-
(2010)
J. Mol. Recognit.
, vol.23
, pp. 173-182
-
-
Durrant, J.D.1
de Oliveira, C.A.F.2
McCammon, J.A.3
-
126
-
-
79952153989
-
Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes
-
Schäfer L.V., de Jong D.H., Holt A., Rzepiela A.J., de Vries A.H., Poolman B., Killian J.A., Marrink S.J. Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:1343-1348.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 1343-1348
-
-
Schäfer, L.V.1
de Jong, D.H.2
Holt, A.3
Rzepiela, A.J.4
de Vries, A.H.5
Poolman, B.6
Killian, J.A.7
Marrink, S.J.8
-
127
-
-
58149181485
-
Lipids on the move: simulations of membrane pores, domains, stalks and curves
-
Marrink S.J., de Vries A.H., Tieleman D.P. Lipids on the move: simulations of membrane pores, domains, stalks and curves. Biochim. Biophys. Acta 2009, 1788:149-168.
-
(2009)
Biochim. Biophys. Acta
, vol.1788
, pp. 149-168
-
-
Marrink, S.J.1
de Vries, A.H.2
Tieleman, D.P.3
-
128
-
-
79958842874
-
Modelling proteins: conformational sampling and reconstruction of folding kinetics
-
Klenin K., Strodel B., Wales D.J., Wenzel W. Modelling proteins: conformational sampling and reconstruction of folding kinetics. Biochim. Biophys. Acta 2010, 1814:977-1000.
-
(2010)
Biochim. Biophys. Acta
, vol.1814
, pp. 977-1000
-
-
Klenin, K.1
Strodel, B.2
Wales, D.J.3
Wenzel, W.4
-
129
-
-
64649084606
-
Molecular dynamics simulations of membrane channels and transporters
-
Khalili-Araghi F., Gumbart J., Wen P.C., Sotomayor M., Tajkhorshid E., Schulten K. Molecular dynamics simulations of membrane channels and transporters. Curr. Opin. Struct. Biol. 2009, 19:128-137.
-
(2009)
Curr. Opin. Struct. Biol.
, vol.19
, pp. 128-137
-
-
Khalili-Araghi, F.1
Gumbart, J.2
Wen, P.C.3
Sotomayor, M.4
Tajkhorshid, E.5
Schulten, K.6
-
130
-
-
49549083949
-
Membrane proteins: molecular dynamics simulations
-
Lindahl E., Sansom M.S.P. Membrane proteins: molecular dynamics simulations. Curr. Opin. Struct. Biol. 2008, 18:425-431.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 425-431
-
-
Lindahl, E.1
Sansom, M.S.P.2
-
131
-
-
23044476985
-
Molecular dynamics simulations of proteins in lipid bilayers
-
Gumbart J., Wang Y., Aksimentiev A., Tajkhorshid E., Schulten K. Molecular dynamics simulations of proteins in lipid bilayers. Curr. Opin. Struct. Biol. 2005, 15:423-431.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 423-431
-
-
Gumbart, J.1
Wang, Y.2
Aksimentiev, A.3
Tajkhorshid, E.4
Schulten, K.5
-
132
-
-
34249930405
-
Protein-folding dynamics: overview of molecular simulation techniques
-
Scheraga H.A., Khalili M., Liwo A. Protein-folding dynamics: overview of molecular simulation techniques. Annu. Rev. Phys. Chem. 2007, 58:57-83.
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, pp. 57-83
-
-
Scheraga, H.A.1
Khalili, M.2
Liwo, A.3
-
133
-
-
76149136021
-
Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
-
Voelz V.A., Bowman G.R., Beauchamp K., Pande V.S. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J. Am. Chem. Soc. 2010, 132:1526-1528.
-
(2010)
J. Am. Chem. Soc.
, vol.132
, pp. 1526-1528
-
-
Voelz, V.A.1
Bowman, G.R.2
Beauchamp, K.3
Pande, V.S.4
-
134
-
-
74049112717
-
Millisecond-scale molecular dynamics simulations on Anton, Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09), ACM, New York
-
D.E. Shaw, R.O. Dror, J.K. Salmon, J.P. Grossman, K.M. Mackenzie, J.A. Bank, C. Young, M.M. Deneroff, B. Batson, K.J. Bowers, E. Chow, M.P. Eastwood, D.J. Ierardi, J.L. Klepeis, J.S. Kuskin, R.H. Larson, K. Lindorff-Larsen, P. Maragakis, M.A. Moraes, S. Piana, Y. Shan, B. Towles, Millisecond-scale molecular dynamics simulations on Anton, Proceedings of the Conference on High Performance Computing, Networking, Storage and Analysis (SC09), ACM, New York, 2009.
-
(2009)
-
-
Shaw, D.E.1
Dror, R.O.2
Salmon, J.K.3
Grossman, J.P.4
Mackenzie, K.M.5
Bank, J.A.6
Young, C.7
Deneroff, M.M.8
Batson, B.9
Bowers, K.J.10
Chow, E.11
Eastwood, M.P.12
Ierardi, D.J.13
Klepeis, J.L.14
Kuskin, J.S.15
Larson, R.H.16
Lindorff-Larsen, K.17
Maragakis, P.18
Moraes, M.A.19
Piana, S.20
Shan, Y.21
Towles, B.22
more..
-
135
-
-
0008901450
-
Relative partition coefficients for organic solutes from fluid simulations
-
Jorgensen W.L., Briggs J.M., Contreras M.L. Relative partition coefficients for organic solutes from fluid simulations. J. Phys. Chem. 1990, 94:1683-1686.
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 1683-1686
-
-
Jorgensen, W.L.1
Briggs, J.M.2
Contreras, M.L.3
-
136
-
-
17844363454
-
An improved nucleic acid parameter set for the GROMOS force field
-
Soares T.A., Hünenberger P.H., Kastenholz M.A., Kräutler V., Lenz T., Lins R.D., Oostenbrink C., van Gunsteren W.F. An improved nucleic acid parameter set for the GROMOS force field. J. Comput. Chem. 2005, 26:725-737.
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 725-737
-
-
Soares, T.A.1
Hünenberger, P.H.2
Kastenholz, M.A.3
Kräutler, V.4
Lenz, T.5
Lins, R.D.6
Oostenbrink, C.7
van Gunsteren, W.F.8
-
137
-
-
1642485164
-
Coarse grained model for semiquantitative lipid simulations
-
Marrink S.J., de Vries A.H., Mark A.E. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 2004, 108:750-760.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 750-760
-
-
Marrink, S.J.1
de Vries, A.H.2
Mark, A.E.3
-
138
-
-
34547474332
-
The MARTINI force field: coarse grained model for biomolecular simulations
-
Marrink S.J., Risselada H.J., Yefimov S., Tieleman D.P., de Vries A.H. The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 2007, 111:7812-7824.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 7812-7824
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
de Vries, A.H.5
-
139
-
-
49449113010
-
The MARTINI coarse-grained force field: extension to proteins
-
Monticelli L., Kandasamy S.K., Periole X., Larson R.G., Tieleman D.P., Marrink S.J. The MARTINI coarse-grained force field: extension to proteins. J. Chem. Theory. Comput. 2008, 4:819-834.
-
(2008)
J. Chem. Theory. Comput.
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
Marrink, S.J.6
-
140
-
-
72749104760
-
Coarse-grained MD simulations and protein-protein interactions: the Cohesin-Dockerin system
-
Hall B.A., Sansom M.S.P. Coarse-grained MD simulations and protein-protein interactions: the Cohesin-Dockerin system. J. Chem. Theory. Comput. 2009, 5:2465-2471.
-
(2009)
J. Chem. Theory. Comput.
, vol.5
, pp. 2465-2471
-
-
Hall, B.A.1
Sansom, M.S.P.2
-
141
-
-
78149432360
-
Simulation of coarse-grained protein-protein interactions with graphics processing units
-
Tunbridge I., Best R.B., Gain J., Kuttel M.M. Simulation of coarse-grained protein-protein interactions with graphics processing units. J. Chem. Theory. Comput. 2010, 6:3588-3600.
-
(2010)
J. Chem. Theory. Comput.
, vol.6
, pp. 3588-3600
-
-
Tunbridge, I.1
Best, R.B.2
Gain, J.3
Kuttel, M.M.4
-
142
-
-
34250378726
-
Lipid-based mechanisms for vesicle fission
-
Markvoort A.J., Smeijers A.F., Pieterse K., van Santen R.A., Hilbers P.A.J. Lipid-based mechanisms for vesicle fission. J. Phys. Chem. B 2007, 111:5719-5725.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 5719-5725
-
-
Markvoort, A.J.1
Smeijers, A.F.2
Pieterse, K.3
van Santen, R.A.4
Hilbers, P.A.J.5
-
143
-
-
33746453289
-
Coarse-grained transmembrane proteins: hydrophobic matching, aggregation, and their effect on fusion
-
Smeijers A.F., Pieterse K., Markvoort A.J., Hilbers P.A.J. Coarse-grained transmembrane proteins: hydrophobic matching, aggregation, and their effect on fusion. J. Phys. Chem. B 2006, 110:13614-13623.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 13614-13623
-
-
Smeijers, A.F.1
Pieterse, K.2
Markvoort, A.J.3
Hilbers, P.A.J.4
-
144
-
-
39149100599
-
Coarse-grained models of protein folding: toy models or predictive tools?
-
Clementi C. Coarse-grained models of protein folding: toy models or predictive tools?. Curr. Opin. Struct. Biol. 2008, 18:10-15.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 10-15
-
-
Clementi, C.1
-
145
-
-
33646126931
-
Effects of disulfide bonds on folding behavior and mechanism of the β-sheet protein tendamistat
-
Qin M., Zhang J., Wang W. Effects of disulfide bonds on folding behavior and mechanism of the β-sheet protein tendamistat. Biophys. J. 2006, 90:272-286.
-
(2006)
Biophys. J.
, vol.90
, pp. 272-286
-
-
Qin, M.1
Zhang, J.2
Wang, W.3
-
146
-
-
55149087047
-
Peptide folding using multiscale coarse-grained models
-
Thorpe I.F., Zhou J., Voth G.A. Peptide folding using multiscale coarse-grained models. J. Phys. Chem. B 2008, 112:13079-13090.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 13079-13090
-
-
Thorpe, I.F.1
Zhou, J.2
Voth, G.A.3
-
147
-
-
33847242278
-
Coarse-grained molecular dynamics simulations of membrane proteins and peptides
-
Bond P.J., Holyoake J., Ivetac A., Khalid S., Sansom M.S.P. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 2007, 157:593-605.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 593-605
-
-
Bond, P.J.1
Holyoake, J.2
Ivetac, A.3
Khalid, S.4
Sansom, M.S.P.5
-
148
-
-
41449119304
-
Coarse-grained MD simulations of membrane protein-bilayer self-assembly
-
Scott K.A., Bond P.J., Ivetac A., Chetwynd A.P., Khalid S., Sansom M.S.P. Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Structure 2008, 16:621-630.
-
(2008)
Structure
, vol.16
, pp. 621-630
-
-
Scott, K.A.1
Bond, P.J.2
Ivetac, A.3
Chetwynd, A.P.4
Khalid, S.5
Sansom, M.S.P.6
-
149
-
-
34848895197
-
Structural determinants of lateral gate opening in the protein translocon
-
Gumbart J., Schulten K. Structural determinants of lateral gate opening in the protein translocon. Biochemistry 2007, 46:11147-11157.
-
(2007)
Biochemistry
, vol.46
, pp. 11147-11157
-
-
Gumbart, J.1
Schulten, K.2
-
150
-
-
45949109759
-
Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations
-
Treptow W., Marrink S.J., Tarek M. Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations. J. Phys. Chem. B 2008, 112:3277-3282.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 3277-3282
-
-
Treptow, W.1
Marrink, S.J.2
Tarek, M.3
-
151
-
-
43149103416
-
Mechanosensitive membrane channels in action
-
Yefimov S., van der Giessen E., Onck P.R., Marrink S.J. Mechanosensitive membrane channels in action. Biophys. J. 2008, 94:2994-3002.
-
(2008)
Biophys. J.
, vol.94
, pp. 2994-3002
-
-
Yefimov, S.1
van der Giessen, E.2
Onck, P.R.3
Marrink, S.J.4
-
152
-
-
70349087354
-
Polarization effects in molecular mechanical force fields
-
Cieplak P., Dupradeau F.Y., Duan Y., Wang J. Polarization effects in molecular mechanical force fields. J. Phys. Condens. Matter 2009, 21:333102.
-
(2009)
J. Phys. Condens. Matter
, vol.21
, pp. 333102
-
-
Cieplak, P.1
Dupradeau, F.Y.2
Duan, Y.3
Wang, J.4
-
153
-
-
51149211502
-
Improved simulation of liquid water by molecular dynamics
-
Stillinger F.H. Improved simulation of liquid water by molecular dynamics. J. Chem. Phys. 1974, 60:1545-1557.
-
(1974)
J. Chem. Phys.
, vol.60
, pp. 1545-1557
-
-
Stillinger, F.H.1
-
155
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., Klein M.L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 1983, 79:926-935.
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
156
-
-
33947139278
-
Setting up and running molecular dynamics simulations of membrane proteins
-
Kandt C., Ash W.L., Tieleman D.P. Setting up and running molecular dynamics simulations of membrane proteins. Methods 2007, 41:475-488.
-
(2007)
Methods
, vol.41
, pp. 475-488
-
-
Kandt, C.1
Ash, W.L.2
Tieleman, D.P.3
-
157
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still W.C., Tempczyk A., Hawley R.C., Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 1990, 112:6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
158
-
-
0034510764
-
Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models
-
Bursulaya B.D., Brooks C.L. Comparative study of the folding free energy landscape of a three-stranded β-sheet protein with explicit and implicit solvent models. J. Phys. Chem. B 2000, 104:12378-12383.
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 12378-12383
-
-
Bursulaya, B.D.1
Brooks, C.L.2
-
159
-
-
0141704162
-
Free energy landscape of protein folding in water: explicit vs. implicit solvent
-
Zhou R. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins 2003, 53:148-161.
-
(2003)
Proteins
, vol.53
, pp. 148-161
-
-
Zhou, R.1
-
160
-
-
42949100258
-
De novo prediction of the structures of M. tuberculosis membrane proteins
-
Bu L., Brooks C.L. De novo prediction of the structures of M. tuberculosis membrane proteins. J. Am. Chem. Soc. 2008, 130:5384-5385.
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 5384-5385
-
-
Bu, L.1
Brooks, C.L.2
-
161
-
-
33846804141
-
Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations
-
Bu L., Im W., Brooks C.L. Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophys. J. 2007, 92:854-863.
-
(2007)
Biophys. J.
, vol.92
, pp. 854-863
-
-
Bu, L.1
Im, W.2
Brooks, C.L.3
-
162
-
-
0242322528
-
An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins
-
Im W., Feig M., Brooks C.L. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophys. J. 2003, 85:2900-2918.
-
(2003)
Biophys. J.
, vol.85
, pp. 2900-2918
-
-
Im, W.1
Feig, M.2
Brooks, C.L.3
-
163
-
-
0017100947
-
Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel A., Levitt M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 1976, 103:227-249.
-
(1976)
J. Mol. Biol.
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
164
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y., Okamoto Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314:141-151.
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
165
-
-
28844494903
-
Coarse-grained model of proteins incorporating atomistic detail of the active site
-
Neri M., Anselmi C., Cascella M., Maritan A., Carloni P. Coarse-grained model of proteins incorporating atomistic detail of the active site. Phys. Rev. Lett. 2005, 95:1-4.
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 1-4
-
-
Neri, M.1
Anselmi, C.2
Cascella, M.3
Maritan, A.4
Carloni, P.5
-
166
-
-
37749005024
-
Microseconds dynamics simulations of the outer-membrane protease T
-
Neri M., Baaden M., Carnevale V., Anselmi C., Maritan A., Carloni P. Microseconds dynamics simulations of the outer-membrane protease T. Biophys. J. 2008, 94:71-78.
-
(2008)
Biophys. J.
, vol.94
, pp. 71-78
-
-
Neri, M.1
Baaden, M.2
Carnevale, V.3
Anselmi, C.4
Maritan, A.5
Carloni, P.6
-
167
-
-
33645277151
-
Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential
-
Neri M., Anselmi C., Carnevale V., Vargiu A.V., Carloni P. Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential. J. Phys. Condens. Matter 2006, 18:S347-S355.
-
(2006)
J. Phys. Condens. Matter
, vol.18
-
-
Neri, M.1
Anselmi, C.2
Carnevale, V.3
Vargiu, A.V.4
Carloni, P.5
-
168
-
-
33748266722
-
Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel
-
Shi Q., Izvekov S., Voth G.A. Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel. J. Phys. Chem. B 2006, 110:15045-15048.
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 15045-15048
-
-
Shi, Q.1
Izvekov, S.2
Voth, G.A.3
-
169
-
-
34447515841
-
From coarse-grain to all-atom: toward multiscale analysis of protein landscapes
-
Heath A.P., Kavraki L.E., Clementi C. From coarse-grain to all-atom: toward multiscale analysis of protein landscapes. Proteins 2007, 646-661.
-
(2007)
Proteins
, pp. 646-661
-
-
Heath, A.P.1
Kavraki, L.E.2
Clementi, C.3
-
170
-
-
70849108762
-
Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations
-
Koga N., Kameda T., Okazaki K., Takada S. Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:18237-18242.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 18237-18242
-
-
Koga, N.1
Kameda, T.2
Okazaki, K.3
Takada, S.4
-
171
-
-
67249145514
-
Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously
-
Li W., Takada S. Self-learning multiscale simulation for achieving high accuracy and high efficiency simultaneously. J. Chem. Phys. 2009, 130:214108.
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 214108
-
-
Li, W.1
Takada, S.2
-
172
-
-
3042801661
-
Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model
-
Felts A.K., Harano Y., Gallicchio E., Levy R.M. Free energy surfaces of beta-hairpin and alpha-helical peptides generated by replica exchange molecular dynamics with the AGBNP implicit solvent model. Proteins 2004, 56:310-321.
-
(2004)
Proteins
, vol.56
, pp. 310-321
-
-
Felts, A.K.1
Harano, Y.2
Gallicchio, E.3
Levy, R.M.4
-
173
-
-
0035909921
-
The free energy landscape for beta hairpin folding in explicit water
-
Zhou R., Berne B.J., Germain R. The free energy landscape for beta hairpin folding in explicit water. Proc. Natl. Acad. Sci. U.S.A. 2001, 98:14931-14936.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 14931-14936
-
-
Zhou, R.1
Berne, B.J.2
Germain, R.3
-
174
-
-
0345133287
-
Folding a protein in a computer: an atomic description of the folding/unfolding of protein A
-
García A.E., Onuchic J.N. Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc. Natl. Acad. Sci. U.S.A. 2003, 100:13898-13903.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 13898-13903
-
-
García, A.E.1
Onuchic, J.N.2
-
175
-
-
33846227108
-
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
-
Kannan S., Zacharias M. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential. Proteins 2007, 66:697-706.
-
(2007)
Proteins
, vol.66
, pp. 697-706
-
-
Kannan, S.1
Zacharias, M.2
-
176
-
-
77957965659
-
Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent
-
Kannan S., Zacharias M. Application of biasing-potential replica-exchange simulations for loop modeling and refinement of proteins in explicit solvent. Proteins 2010, 2809-2819.
-
(2010)
Proteins
, pp. 2809-2819
-
-
Kannan, S.1
Zacharias, M.2
-
178
-
-
0342424187
-
Fast prediction and visualization of protein binding pockets with PASS
-
Brady G.P., Stouten P.F. Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des. 2000, 14:383-401.
-
(2000)
J. Comput. Aided Mol. Des.
, vol.14
, pp. 383-401
-
-
Brady, G.P.1
Stouten, P.F.2
-
179
-
-
33747818007
-
CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
-
Dundas J., Ouyang Z., Tseng J., Binkowski A., Turpaz Y., Liang J. CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res. 2006, 34:W116-W118.
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Dundas, J.1
Ouyang, Z.2
Tseng, J.3
Binkowski, A.4
Turpaz, Y.5
Liang, J.6
-
180
-
-
0031370977
-
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins
-
Hendlich M., Rippmann F., Barnickel G. LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model. 1997, 15:359-389.
-
(1997)
J. Mol. Graph. Model.
, vol.15
, pp. 359-389
-
-
Hendlich, M.1
Rippmann, F.2
Barnickel, G.3
-
181
-
-
33750029942
-
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation
-
Huang B., Schroeder M. LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation. BMC Struct. Biol. 2006, 6:19.
-
(2006)
BMC Struct. Biol.
, vol.6
, pp. 19
-
-
Huang, B.1
Schroeder, M.2
-
182
-
-
0028881975
-
SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions
-
Laskowski R.A. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph. 1995, 13:323-328.
-
(1995)
J. Mol. Graph.
, vol.13
, pp. 323-328
-
-
Laskowski, R.A.1
-
183
-
-
0027053611
-
POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
-
Levitt D.G., Banaszak L.J. POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph. 1992, 10:229-234.
-
(1992)
J. Mol. Graph.
, vol.10
, pp. 229-234
-
-
Levitt, D.G.1
Banaszak, L.J.2
-
184
-
-
77954266960
-
SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison
-
Ren J., Xie L., Li W.W., Bourne P.E. SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison. Nucleic Acids Res. 2010, 38:W441-W444.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Ren, J.1
Xie, L.2
Li, W.W.3
Bourne, P.E.4
-
185
-
-
34547341277
-
PocketPicker: analysis of ligand binding-sites with shape descriptors
-
Weisel M., Proschak E., Schneider G. PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem. Cent. J. 2007, 1.
-
(2007)
Chem. Cent. J.
, vol.1
-
-
Weisel, M.1
Proschak, E.2
Schneider, G.3
-
186
-
-
0036681416
-
Scoring residue conservation
-
Valdar W.S.J. Scoring residue conservation. Proteins 2002, 48:227-241.
-
(2002)
Proteins
, vol.48
, pp. 227-241
-
-
Valdar, W.S.J.1
-
187
-
-
74549149999
-
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
-
Capra J.A., Laskowski R.A., Thornton J.M., Singh M., Funkhouser T.A. Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput. Biol. 2009, 5:e1000585.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Capra, J.A.1
Laskowski, R.A.2
Thornton, J.M.3
Singh, M.4
Funkhouser, T.A.5
-
188
-
-
0035025191
-
DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases
-
Ewing T.J., Makino S., Skillman A.G., Kuntz I.D. DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aided Mol. Des. 2001, 15:411-428.
-
(2001)
J. Comput. Aided Mol. Des.
, vol.15
, pp. 411-428
-
-
Ewing, T.J.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
189
-
-
0029705324
-
Automated docking of flexible ligands: applications of AutoDock
-
Goodsell D.S., Morris G.M., Olson A.J. Automated docking of flexible ligands: applications of AutoDock. J. Mol. Recognit. 1996, 9:1-5.
-
(1996)
J. Mol. Recognit.
, vol.9
, pp. 1-5
-
-
Goodsell, D.S.1
Morris, G.M.2
Olson, A.J.3
-
190
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19:1639-1662.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
191
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones G., Willett P., Glen R.C., Leach A.R., Taylor R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267:727-748.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
192
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
-
Jones G., Willett P., Glen R. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 1995, 245:43-53.
-
(1995)
J. Mol. Biol.
, vol.245
, pp. 43-53
-
-
Jones, G.1
Willett, P.2
Glen, R.3
-
193
-
-
33750124980
-
Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
Friesner R.A., Murphy R.B., Repasky M.P., Frye L.L., Greenwood J.R., Halgren T.A., Sanschagrin P.C., Mainz D.T. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 2006:6177-6196.
-
(2006)
J. Med. Chem.
, vol.2006
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
194
-
-
12144289984
-
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner R.A., Banks J.L., Murphy R.B., Halgren T.A., Klicic J.J., Mainz D.T., Repasky M.P., Knoll E.H., Shelley M., Perry J.K., Shaw D.E., Francis P., Shenkin P. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 2004, 47:1739-1749.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.13
-
195
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey M., Kramer B., Lengauer T., Klebe G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261:470-489.
-
(1996)
J. Mol. Biol.
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
196
-
-
84986522918
-
ICM-A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation
-
Abagyan R., Totrov M., Kuznetsov D. ICM-A new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 1994, 15:488-506.
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
197
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford P.J. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem. 1985, 28:849-857.
-
(1985)
J. Med. Chem.
, vol.28
, pp. 849-857
-
-
Goodford, P.J.1
-
198
-
-
17144368025
-
Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking
-
de Graaf C., Pospisil P., Pos W., Folkers G., Vermeulen N.P.E. Binding mode prediction of cytochrome p450 and thymidine kinase protein-ligand complexes by consideration of water and rescoring in automated docking. J. Med. Chem. 2005, 48:2308-2318.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2308-2318
-
-
de Graaf, C.1
Pospisil, P.2
Pos, W.3
Folkers, G.4
Vermeulen, N.P.E.5
-
199
-
-
0032961895
-
The particle concept: placing discrete water molecules during protein-ligand docking predictions
-
Rarey M., Kramer B., Lengauer T. The particle concept: placing discrete water molecules during protein-ligand docking predictions. Proteins 1999, 34:17-28.
-
(1999)
Proteins
, vol.34
, pp. 17-28
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
200
-
-
84858622848
-
Protein-ligand docking: current status and future
-
Sousa F., Fernandes P.A., Joa M. Protein-ligand docking: current status and future. Bioinformatics 2006, 26:15-26.
-
(2006)
Bioinformatics
, vol.26
, pp. 15-26
-
-
Sousa, F.1
Fernandes, P.A.2
Joa, M.3
-
201
-
-
79951996670
-
Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
-
Hou T., Wang J., Li Y., Wang W. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking. J. Comput. Chem. 2010, 32:866-877.
-
(2010)
J. Comput. Chem.
, vol.32
, pp. 866-877
-
-
Hou, T.1
Wang, J.2
Li, Y.3
Wang, W.4
-
202
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
Warren G.L., Andrews C.W., Capelli A.M., Clarke B., LaLonde J., Lambert M.H., Lindvall M., Nevins N., Semus S.F., Senger S., Tedesco G., Wall I.D., Woolven J.M., Peishoff C.E., Head M.S. A critical assessment of docking programs and scoring functions. J. Med. Chem. 2006, 49:5912-5931.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
203
-
-
23044513878
-
Comparing protein-ligand docking programs is difficult
-
Cole J.C., Murray C.W., Nissink J.W.M., Taylor R.D., Taylor R. Comparing protein-ligand docking programs is difficult. Proteins 2005, 60:325-332.
-
(2005)
Proteins
, vol.60
, pp. 325-332
-
-
Cole, J.C.1
Murray, C.W.2
Nissink, J.W.M.3
Taylor, R.D.4
Taylor, R.5
-
204
-
-
67650097331
-
Comparison of several molecular docking programs: pose prediction and virtual screening accuracy
-
Cross J.B., Thompson D.C., Rai B.K., Baber J.C., Fan K.Y., Hu Y., Humblet C. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J. Chem. Inf. Model. 2009, 49:1455-1474.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1455-1474
-
-
Cross, J.B.1
Thompson, D.C.2
Rai, B.K.3
Baber, J.C.4
Fan, K.Y.5
Hu, Y.6
Humblet, C.7
-
205
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
-
Kellenberger E., Rodrigo J., Muller P., Rognan D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 2004, 57:225-242.
-
(2004)
Proteins
, vol.57
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
206
-
-
0035289779
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
Lipinski C.A., Lombardo F., Dominy B.W., Feeney P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 2001, 46:3-26.
-
(2001)
Adv. Drug Deliv. Rev.
, vol.46
, pp. 3-26
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
207
-
-
13844312649
-
ZINC - a free database of commercially available compounds for virtual screening
-
Irwin J.J., Shoichet B.K. ZINC - a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 2005, 45:177-182.
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
208
-
-
77954818699
-
Pharmacophore modeling and applications in drug discovery: challenges and recent advances
-
Yang S.-Y. Pharmacophore modeling and applications in drug discovery: challenges and recent advances. Drug Discov. Today 2010, 15:444-450.
-
(2010)
Drug Discov. Today
, vol.15
, pp. 444-450
-
-
Yang, S.-Y.1
-
209
-
-
79952196849
-
Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design
-
Ebalunode J.O., Zheng W., Tropsha A. Application of QSAR and shape pharmacophore modeling approaches for targeted chemical library design. Methods Mol. Biol. 2011, 685:111-133.
-
(2011)
Methods Mol. Biol.
, vol.685
, pp. 111-133
-
-
Ebalunode, J.O.1
Zheng, W.2
Tropsha, A.3
-
210
-
-
36549030345
-
Multi-dimensional QSAR in drug discovery
-
Lill M.A. Multi-dimensional QSAR in drug discovery. Drug Discov. Today 2007, 12:1013-1017.
-
(2007)
Drug Discov. Today
, vol.12
, pp. 1013-1017
-
-
Lill, M.A.1
-
211
-
-
48749125396
-
Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening
-
Tanrikulu Y., Schneider G. Pseudoreceptor models in drug design: bridging ligand- and receptor-based virtual screening. Nat. Rev. Drug Discov. 2008, 7:667-677.
-
(2008)
Nat. Rev. Drug Discov.
, vol.7
, pp. 667-677
-
-
Tanrikulu, Y.1
Schneider, G.2
-
212
-
-
77955549192
-
Pulmonary surfactant pathophysiology: current models and open questions
-
Perez-Gil J., Weaver T.E. Pulmonary surfactant pathophysiology: current models and open questions. Physiology. 2010, 25:132-141.
-
(2010)
Physiology.
, vol.25
, pp. 132-141
-
-
Perez-Gil, J.1
Weaver, T.E.2
-
213
-
-
52049111368
-
Current perspectives in pulmonary surfactant - inhibition, enhancement and evaluation
-
Zuo Y.Y., Veldhuizen R.A.W., Neumann A.W., Petersen N.O., Possmayer F. Current perspectives in pulmonary surfactant - inhibition, enhancement and evaluation. Biochim. Biophys. Acta 2008, 1778:1947-1977.
-
(2008)
Biochim. Biophys. Acta
, vol.1778
, pp. 1947-1977
-
-
Zuo, Y.Y.1
Veldhuizen, R.A.W.2
Neumann, A.W.3
Petersen, N.O.4
Possmayer, F.5
-
214
-
-
0031740674
-
Pulmonary surfactant: functions and molecular composition
-
Goerke J. Pulmonary surfactant: functions and molecular composition. Biochim. Biophys. Acta 1998, 1408:79-89.
-
(1998)
Biochim. Biophys. Acta
, vol.1408
, pp. 79-89
-
-
Goerke, J.1
-
215
-
-
0032135111
-
Collectins and pulmonary host defense
-
Crouch E.C. Collectins and pulmonary host defense. Am. J. Respir. Cell Mol. Biol. 1998, 19:177-201.
-
(1998)
Am. J. Respir. Cell Mol. Biol.
, vol.19
, pp. 177-201
-
-
Crouch, E.C.1
-
216
-
-
0033635798
-
The role of surfactant proteins in DPPC enrichment of surface films
-
Veldhuizen E.J., Batenburg J.J., van Golde L.M., Haagsman H.P. The role of surfactant proteins in DPPC enrichment of surface films. Biophys. J. 2000, 79:3164-3171.
-
(2000)
Biophys. J.
, vol.79
, pp. 3164-3171
-
-
Veldhuizen, E.J.1
Batenburg, J.J.2
van Golde, L.M.3
Haagsman, H.P.4
-
218
-
-
0028174249
-
A direct test of the "squeeze-out" hypothesis of lung surfactant function. External reflection FT-IR at the air/water interface
-
Pastrana-Rios B., Flach C.R., Brauner J.W., Mautone A.J., Mendelsohn R. A direct test of the "squeeze-out" hypothesis of lung surfactant function. External reflection FT-IR at the air/water interface. Biochemistry 1994, 33:5121-5127.
-
(1994)
Biochemistry
, vol.33
, pp. 5121-5127
-
-
Pastrana-Rios, B.1
Flach, C.R.2
Brauner, J.W.3
Mautone, A.J.4
Mendelsohn, R.5
-
219
-
-
0014402453
-
The surface properties of pure phospholipids in relation to those of lung extracts
-
Watkins J.C. The surface properties of pure phospholipids in relation to those of lung extracts. Biochim. Biophys. Acta 1968, 152:293-306.
-
(1968)
Biochim. Biophys. Acta
, vol.152
, pp. 293-306
-
-
Watkins, J.C.1
-
220
-
-
32044441404
-
Structures of pulmonary surfactant films adsorbed to an air-liquid interface in vitro
-
Bachofen H., Gerber U., Gehr P., Amrein M., Schürch S. Structures of pulmonary surfactant films adsorbed to an air-liquid interface in vitro. Biochim. Biophys. Acta 2005, 1720:59-72.
-
(2005)
Biochim. Biophys. Acta
, vol.1720
, pp. 59-72
-
-
Bachofen, H.1
Gerber, U.2
Gehr, P.3
Amrein, M.4
Schürch, S.5
-
221
-
-
0037077194
-
Multilayer formation upon compression of surfactant monolayers depends on protein concentration as well as lipid composition. An atomic force microscopy study
-
Diemel R.V., Snel M.M.E., Waring A.J., Walther F.J., van Golde L.M.G., Putz G., Haagsman H.P., Batenburg J.J. Multilayer formation upon compression of surfactant monolayers depends on protein concentration as well as lipid composition. An atomic force microscopy study. J. Biol. Chem. 2002, 277:21179-21188.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 21179-21188
-
-
Diemel, R.V.1
Snel, M.M.E.2
Waring, A.J.3
Walther, F.J.4
van Golde, L.M.G.5
Putz, G.6
Haagsman, H.P.7
Batenburg, J.J.8
-
222
-
-
33846371945
-
Multilayers at the surface of solutions of exogenous lung surfactant: direct observation by neutron reflection
-
Follows D., Tiberg F., Thomas R.K., Larsson M. Multilayers at the surface of solutions of exogenous lung surfactant: direct observation by neutron reflection. Biochim. Biophys. Acta 2007, 1768:228-235.
-
(2007)
Biochim. Biophys. Acta
, vol.1768
, pp. 228-235
-
-
Follows, D.1
Tiberg, F.2
Thomas, R.K.3
Larsson, M.4
-
223
-
-
0029026845
-
The surface-associated surfactant reservoir in the alveolar lining
-
Schürch S., Qanbar R., Bachofen H., Possmayer F. The surface-associated surfactant reservoir in the alveolar lining. Biol. Neonate 1995, 67(Suppl 1):61-76.
-
(1995)
Biol. Neonate
, vol.67
, Issue.SUPPL. 1
, pp. 61-76
-
-
Schürch, S.1
Qanbar, R.2
Bachofen, H.3
Possmayer, F.4
-
224
-
-
10044228172
-
More than a monolayer: relating lung surfactant structure and mechanics to composition
-
Alonso C., Alig T., Yoon J., Bringezu F., Warriner H., Zasadzinski J.A. More than a monolayer: relating lung surfactant structure and mechanics to composition. Biophys. J. 2004, 87:4188-4202.
-
(2004)
Biophys. J.
, vol.87
, pp. 4188-4202
-
-
Alonso, C.1
Alig, T.2
Yoon, J.3
Bringezu, F.4
Warriner, H.5
Zasadzinski, J.A.6
-
225
-
-
48949100335
-
Surfactant-replacement therapy for respiratory distress syndrome in the preterm and term neonate: congratulations and corrections
-
Moya F., Sinha S., D'Agostino R.B. Surfactant-replacement therapy for respiratory distress syndrome in the preterm and term neonate: congratulations and corrections. Pediatrics 2008, 121:1290-1291.
-
(2008)
Pediatrics
, vol.121
, pp. 1290-1291
-
-
Moya, F.1
Sinha, S.2
D'Agostino, R.B.3
-
226
-
-
38849125645
-
Surfactant-replacement therapy for respiratory distress in the preterm and term neonate
-
Engle W.A. Surfactant-replacement therapy for respiratory distress in the preterm and term neonate. Pediatrics 2008, 121:419-432.
-
(2008)
Pediatrics
, vol.121
, pp. 419-432
-
-
Engle, W.A.1
-
227
-
-
55549106085
-
Molecular dynamics simulations of lung surfactant lipid monolayers
-
Rose D., Rendell J., Lee D., Nag K., Booth V. Molecular dynamics simulations of lung surfactant lipid monolayers. Biophys. Chem. 2008, 138:67-77.
-
(2008)
Biophys. Chem.
, vol.138
, pp. 67-77
-
-
Rose, D.1
Rendell, J.2
Lee, D.3
Nag, K.4
Booth, V.5
-
228
-
-
33846159133
-
Atomistic simulations of Langmuir monolayer collapse
-
Lorenz C.D., Travesset A. Atomistic simulations of Langmuir monolayer collapse. Langmuir 2006, 22:10016-10024.
-
(2006)
Langmuir
, vol.22
, pp. 10016-10024
-
-
Lorenz, C.D.1
Travesset, A.2
-
229
-
-
0036384267
-
Specific mode of interaction between components of model pulmonary surfactants using computer simulations
-
Kaznessis Y.N., Kim S., Larson R.G. Specific mode of interaction between components of model pulmonary surfactants using computer simulations. J. Mol. Biol. 2002, 322:569-582.
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 569-582
-
-
Kaznessis, Y.N.1
Kim, S.2
Larson, R.G.3
-
230
-
-
21244504685
-
Molecular dynamics study of the lung surfactant peptide SP-B1-25 with DPPC monolayers: insights into interactions and peptide position and orientation
-
Kandasamy S.K., Larson R.G. Molecular dynamics study of the lung surfactant peptide SP-B1-25 with DPPC monolayers: insights into interactions and peptide position and orientation. Biophys. J. 2005, 88:1577-1592.
-
(2005)
Biophys. J.
, vol.88
, pp. 1577-1592
-
-
Kandasamy, S.K.1
Larson, R.G.2
-
231
-
-
28444478451
-
Molecular dynamics simulations of the anchoring and tilting of the lung-surfactant peptide SP-B1-25 in palmitic acid monolayers
-
Lee H., Kandasamy S.K., Larson R.G. Molecular dynamics simulations of the anchoring and tilting of the lung-surfactant peptide SP-B1-25 in palmitic acid monolayers. Biophys. J. 2005, 89:3807-3821.
-
(2005)
Biophys. J.
, vol.89
, pp. 3807-3821
-
-
Lee, H.1
Kandasamy, S.K.2
Larson, R.G.3
-
232
-
-
0037379662
-
Molecular dynamics simulations of a pulmonary surfactant protein B peptide in a lipid monolayer
-
Freites J.A., Choi Y., Tobias D.J. Molecular dynamics simulations of a pulmonary surfactant protein B peptide in a lipid monolayer. Biophys. J. 2003, 84:2169-2180.
-
(2003)
Biophys. J.
, vol.84
, pp. 2169-2180
-
-
Freites, J.A.1
Choi, Y.2
Tobias, D.J.3
-
233
-
-
0348197881
-
Molecular dynamics investigations of lipid Langmuir monolayers using a coarse-grain model
-
Nielsen S.O., Lopez C.F., Moore P.B., Shelley J.C., Klein M.L. Molecular dynamics investigations of lipid Langmuir monolayers using a coarse-grain model. J. Phys. Chem. B 2003, 107:13911-13917.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 13911-13917
-
-
Nielsen, S.O.1
Lopez, C.F.2
Moore, P.B.3
Shelley, J.C.4
Klein, M.L.5
-
234
-
-
36849085363
-
The molecular mechanism of monolayer-bilayer transformations of lung surfactant from molecular dynamics simulations
-
Baoukina S., Monticelli L., Amrein M., Tieleman D.P. The molecular mechanism of monolayer-bilayer transformations of lung surfactant from molecular dynamics simulations. Biophys. J. 2007, 93:3775-3782.
-
(2007)
Biophys. J.
, vol.93
, pp. 3775-3782
-
-
Baoukina, S.1
Monticelli, L.2
Amrein, M.3
Tieleman, D.P.4
-
235
-
-
37249073561
-
Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations
-
Baoukina S., Monticelli L., Marrink S.J., Tieleman D.P. Pressure-area isotherm of a lipid monolayer from molecular dynamics simulations. Langmuir 2007, 23:12617-12623.
-
(2007)
Langmuir
, vol.23
, pp. 12617-12623
-
-
Baoukina, S.1
Monticelli, L.2
Marrink, S.J.3
Tieleman, D.P.4
-
236
-
-
49449107938
-
The molecular mechanism of lipid monolayer collapse
-
Baoukina S., Monticelli L., Risselada H.J., Marrink S.J., Tieleman D.P. The molecular mechanism of lipid monolayer collapse. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:10803-10808.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 10803-10808
-
-
Baoukina, S.1
Monticelli, L.2
Risselada, H.J.3
Marrink, S.J.4
Tieleman, D.P.5
-
237
-
-
62349116491
-
Molecular dynamics study of the effect of cholesterol on the properties of lipid monolayers at low surface tensions
-
Laing C., Baoukina S., Tieleman D.P. Molecular dynamics study of the effect of cholesterol on the properties of lipid monolayers at low surface tensions. Phys. Chem. Chem. Phys. 2009, 11:1916-1922.
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 1916-1922
-
-
Laing, C.1
Baoukina, S.2
Tieleman, D.P.3
-
238
-
-
77954658153
-
Folding of lipid monolayers containing lung surfactant proteins SP-B(1-25) and SP-C studied via coarse-grained molecular dynamics simulations
-
Duncan S.L., Larson R.G. Folding of lipid monolayers containing lung surfactant proteins SP-B(1-25) and SP-C studied via coarse-grained molecular dynamics simulations. Biochim. Biophys. Acta 2010, 1798:1632-1650.
-
(2010)
Biochim. Biophys. Acta
, vol.1798
, pp. 1632-1650
-
-
Duncan, S.L.1
Larson, R.G.2
-
239
-
-
0038024615
-
The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
-
Fredriksson R., Lagerström M.C., Lundin L.-G., Schiöth H.B. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol. Pharmacol. 2003, 63:1256-1272.
-
(2003)
Mol. Pharmacol.
, vol.63
, pp. 1256-1272
-
-
Fredriksson, R.1
Lagerström, M.C.2
Lundin, L.-G.3
Schiöth, H.B.4
-
240
-
-
36448995359
-
2-adrenergic G protein-coupled receptor
-
2-adrenergic G protein-coupled receptor. Science 2007, 318:1258-1265.
-
(2007)
Science
, vol.318
, pp. 1258-1265
-
-
Cherezov, V.1
Rosenbaum, D.M.2
Hanson, M.A.3
Rasmussen, S.G.F.4
Thian, F.S.5
Kobilka, T.S.6
Choi, H.J.7
Kuhn, P.8
Weis, W.I.9
Koblika, B.K.10
Stevens, R.C.11
-
241
-
-
47949129742
-
Structure of a β1-adrenergic G-protein-coupled receptor
-
Warne T., Serrano-Vega M.J., Baker J.G., Moukhametzianov R., Edwards P.C., Henderson R., Leslie A.G.W., Tate C.G., Schertler G.F.X. Structure of a β1-adrenergic G-protein-coupled receptor. Nature 2008, 454:486-491.
-
(2008)
Nature
, vol.454
, pp. 486-491
-
-
Warne, T.1
Serrano-Vega, M.J.2
Baker, J.G.3
Moukhametzianov, R.4
Edwards, P.C.5
Henderson, R.6
Leslie, A.G.W.7
Tate, C.G.8
Schertler, G.F.X.9
-
242
-
-
0034604451
-
Crystal structure of rhodopsin: a G protein-coupled receptor
-
Palczewski K., Kumasaka T., Hori T., Behnke C.A., Motoshima H., Fox B.A., Le Trong I., Teller D.C., Okada T., Stenkamp R.E., Yamamoto M., Miyano M. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 2000, 289:739-745.
-
(2000)
Science
, vol.289
, pp. 739-745
-
-
Palczewski, K.1
Kumasaka, T.2
Hori, T.3
Behnke, C.A.4
Motoshima, H.5
Fox, B.A.6
Le Trong, I.7
Teller, D.C.8
Okada, T.9
Stenkamp, R.E.10
Yamamoto, M.11
Miyano, M.12
-
243
-
-
56749103466
-
2A adenosine receptor bound to an antagonist
-
2A adenosine receptor bound to an antagonist. Science 2008, 322:1211-1217.
-
(2008)
Science
, vol.322
, pp. 1211-1217
-
-
Jaakola, V.P.1
Griffith, M.T.2
Hanson, M.A.3
Cherezov, V.4
Chien, E.Y.T.5
Lane, J.R.6
Chien, E.Y.T.7
Lane, J.R.8
Ijzerman, A.P.9
Stevens, R.C.10
-
244
-
-
85027927015
-
Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists
-
Wu B., Chien E.Y.T., Mol C.D., Fenalti G., Liu W., Katritch V., Abagyan R., Brooun A., Wells P., Bi F.C., Hamel D.J., Kuhn P., Handel T.M., Cherezov V., Stevens R.C. Structures of the CXCR4 chemokine GPCR with small-molecule and cyclic peptide antagonists. Science 2010, 330:1066-1071.
-
(2010)
Science
, vol.330
, pp. 1066-1071
-
-
Wu, B.1
Chien, E.Y.T.2
Mol, C.D.3
Fenalti, G.4
Liu, W.5
Katritch, V.6
Abagyan, R.7
Brooun, A.8
Wells, P.9
Bi, F.C.10
Hamel, D.J.11
Kuhn, P.12
Handel, T.M.13
Cherezov, V.14
Stevens, R.C.15
-
245
-
-
78449305788
-
Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist
-
Chien E.Y.T., Liu W., Zhao Q., Katritch V., Won Han G., Hanson M.A., Shi L., Newman A.H., Javitch J.A., Cherezov V., Stevens R.C. Structure of the human dopamine D3 receptor in complex with a D2/D3 selective antagonist. Science 2010, 330:1091-1095.
-
(2010)
Science
, vol.330
, pp. 1091-1095
-
-
Chien, E.Y.T.1
Liu, W.2
Zhao, Q.3
Katritch, V.4
Won Han, G.5
Hanson, M.A.6
Shi, L.7
Newman, A.H.8
Javitch, J.A.9
Cherezov, V.10
Stevens, R.C.11
-
246
-
-
47049130668
-
Crystal structure of the ligand-free G-protein-coupled receptor opsin
-
Park J.H., Scheerer P., Hofmann K.P., Choe H.-W., Ernst O.P. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 2008, 454:183-187.
-
(2008)
Nature
, vol.454
, pp. 183-187
-
-
Park, J.H.1
Scheerer, P.2
Hofmann, K.P.3
Choe, H.-W.4
Ernst, O.P.5
-
247
-
-
78651411166
-
2 adrenoceptor
-
2 adrenoceptor. Nature 2011, 469:175-180.
-
(2011)
Nature
, vol.469
, pp. 175-180
-
-
Rasmussen, S.G.F.1
Choi, H.-J.2
Fung, J.J.3
Pardon, E.4
Casarosa, P.5
Chae, P.S.6
Devree, B.T.7
Rosenbaum, D.M.8
Thian, F.S.9
Kobilka, T.S.10
Schnapp, A.11
Konetzki, I.12
Sunahara, R.K.13
Gellman, S.H.14
Pautsch, A.15
Steyaert, J.16
Weis, W.I.17
Kobilka, B.K.18
-
248
-
-
78651405537
-
The structural basis for agonist and partial agonist action on a β1-adrenergic receptor
-
Warne T., Moukhametzianov R., Baker J.G., Nehmé R., Edwards P.C., Leslie A.G.W., Schertler G.F.X., Tate C.G. The structural basis for agonist and partial agonist action on a β1-adrenergic receptor. Nature 2011, 469:241-244.
-
(2011)
Nature
, vol.469
, pp. 241-244
-
-
Warne, T.1
Moukhametzianov, R.2
Baker, J.G.3
Nehmé, R.4
Edwards, P.C.5
Leslie, A.G.W.6
Schertler, G.F.X.7
Tate, C.G.8
-
249
-
-
79960070651
-
Structure of the human histamine H1 receptor complex with doxepin
-
Shimamura T., Shiroishi M., Weyand S., Tsujimoto H., Winter G., Katritch V., Abagyan R., Cherezov V., Liu W., Han G.W., Kobayashi T., Stevens R.C., Iwata S. Structure of the human histamine H1 receptor complex with doxepin. Nature 2011, 475:65-70.
-
(2011)
Nature
, vol.475
, pp. 65-70
-
-
Shimamura, T.1
Shiroishi, M.2
Weyand, S.3
Tsujimoto, H.4
Winter, G.5
Katritch, V.6
Abagyan, R.7
Cherezov, V.8
Liu, W.9
Han, G.W.10
Kobayashi, T.11
Stevens, R.C.12
Iwata, S.13
-
250
-
-
79954782236
-
2A adenosine receptor
-
2A adenosine receptor. Science 2011, 332:322-327.
-
(2011)
Science
, vol.332
, pp. 322-327
-
-
Xu, F.1
Wu, H.2
Katritch, V.3
Han, G.W.4
Jacobson, K.A.5
Gao, Z.-G.6
Cherezov, V.7
Stevens, R.C.8
-
251
-
-
77954033984
-
New therapies for asthma: is there any progress?
-
Barnes P.J. New therapies for asthma: is there any progress?. Trends Pharmacol. Sci. 2010, 31:335-343.
-
(2010)
Trends Pharmacol. Sci.
, vol.31
, pp. 335-343
-
-
Barnes, P.J.1
-
253
-
-
78651399683
-
2 adrenoceptor complex
-
2 adrenoceptor complex. Nature 2011, 469:236-240.
-
(2011)
Nature
, vol.469
, pp. 236-240
-
-
Rosenbaum, D.M.1
Zhang, C.2
Lyons, J.A.3
Holl, R.4
Aragao, D.5
Arlow, D.H.6
Rasmussen, S.G.F.7
Choi, H.J.8
DeVree, B.T.9
Sunahara, R.K.10
Chae, P.S.11
Gellman, S.H.12
Dror, R.O.13
Shaw, D.E.14
Weis, W.I.15
Caffrey, M.16
Gmeiner, P.17
Kobilka, B.K.18
-
254
-
-
80052001378
-
Pathway and mechanism of drug binding to G-protein-coupled receptors
-
Dror R.O., Pan a C., Arlow D.H., Borhani D.W., Maragakis P., Shan Y., et al. Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc. Natl. Acad. Sci. U.S.A. 2011, 2-7.
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, pp. 2-7
-
-
Dror, R.O.1
Pan, A.C.2
Arlow, D.H.3
Borhani, D.W.4
Maragakis, P.5
Shan, Y.6
-
255
-
-
0035800850
-
Activation of the β2-adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6
-
Ballesteros J.A., Jensen A.D., Liapakis G., Rasmussen S.G.F., Shi L., Gether U., Javitch J.A. Activation of the β2-adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6. J. Biol. Chem. 2001, 276:29171-29177.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 29171-29177
-
-
Ballesteros, J.A.1
Jensen, A.D.2
Liapakis, G.3
Rasmussen, S.G.F.4
Shi, L.5
Gether, U.6
Javitch, J.A.7
-
256
-
-
63849294621
-
Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations
-
Dror R.O., Arlow D.H., Borhani D.W., Jensen M.Ø., Piana S., Shaw D.E. Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. Proc. Natl. Acad. Sci. U.S.A. 2009, 106:4689-4694.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 4689-4694
-
-
Dror, R.O.1
Arlow, D.H.2
Borhani, D.W.3
Jensen, M.Ø.4
Piana, S.5
Shaw, D.E.6
-
258
-
-
0031774720
-
International Union of Pharmacology. XVII. Classification of muscarinic acetylcholine receptors
-
Caulfield M.P., Birdsall N.J. International Union of Pharmacology. XVII. Classification of muscarinic acetylcholine receptors. Pharmacol. Rev. 1998, 50:279-290.
-
(1998)
Pharmacol. Rev.
, vol.50
, pp. 279-290
-
-
Caulfield, M.P.1
Birdsall, N.J.2
-
259
-
-
33745218112
-
Muscarinic receptor signaling in the pathophysiology of asthma and COPD
-
Gosens R., Zaagsma J., Meurs H., Halayko A.J. Muscarinic receptor signaling in the pathophysiology of asthma and COPD. Respir. Res. 2006, 7.
-
(2006)
Respir. Res.
, vol.7
-
-
Gosens, R.1
Zaagsma, J.2
Meurs, H.3
Halayko, A.J.4
-
260
-
-
0025191514
-
3 receptors mediate contraction of human central and peripheral airway smooth muscle
-
3 receptors mediate contraction of human central and peripheral airway smooth muscle. Pulm. Pharmacol. 1990, 3:47-51.
-
(1990)
Pulm. Pharmacol.
, vol.3
, pp. 47-51
-
-
Roffel, A.F.1
Elzinga, C.R.2
Zaagsma, J.3
-
261
-
-
0024850599
-
A muscarinic agonist inhibits reflex bronchoconstriction in normal but not in asthmatic subjects
-
Minette P.A., Lammers J.W., Dixon C.M., McCusker M.T., Barnes P.J. A muscarinic agonist inhibits reflex bronchoconstriction in normal but not in asthmatic subjects. J. Appl. Physiol. 1989, 67:2461-2465.
-
(1989)
J. Appl. Physiol.
, vol.67
, pp. 2461-2465
-
-
Minette, P.A.1
Lammers, J.W.2
Dixon, C.M.3
McCusker, M.T.4
Barnes, P.J.5
-
263
-
-
33745020177
-
Muscarinic receptors: a comparative analysis of structural features and binding modes through homology modelling and molecular docking
-
Pedretti A., Vistoli G., Marconi C., Testa B. Muscarinic receptors: a comparative analysis of structural features and binding modes through homology modelling and molecular docking. Chem. Biodivers. 2006, 3:481-501.
-
(2006)
Chem. Biodivers.
, vol.3
, pp. 481-501
-
-
Pedretti, A.1
Vistoli, G.2
Marconi, C.3
Testa, B.4
-
264
-
-
65549169007
-
3D-QSAR studies of 2,2-diphenylpropionates to aid discovery of novel potent muscarinic antagonists
-
Bhattacharjee A.K., Gordon J.A., Marek E., Campbell A., Gordon R.K. 3D-QSAR studies of 2,2-diphenylpropionates to aid discovery of novel potent muscarinic antagonists. Bioorg. Med. Chem. 2009, 17:3999-4012.
-
(2009)
Bioorg. Med. Chem.
, vol.17
, pp. 3999-4012
-
-
Bhattacharjee, A.K.1
Gordon, J.A.2
Marek, E.3
Campbell, A.4
Gordon, R.K.5
-
265
-
-
35648945337
-
CXCR7 (RDC1) promotes breast and lung tumor growth in vivo and is expressed on tumor-associated vasculature
-
Miao Z., Luker K.E., Summers B.C., Berahovich R., Bhojani M.S., Rehemtulla A., Kleer C.G., Essner J.J., Nasevicius A., Luker G.D., Howard M.C., Schall T.J. CXCR7 (RDC1) promotes breast and lung tumor growth in vivo and is expressed on tumor-associated vasculature. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:15735-15740.
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 15735-15740
-
-
Miao, Z.1
Luker, K.E.2
Summers, B.C.3
Berahovich, R.4
Bhojani, M.S.5
Rehemtulla, A.6
Kleer, C.G.7
Essner, J.J.8
Nasevicius, A.9
Luker, G.D.10
Howard, M.C.11
Schall, T.J.12
-
266
-
-
27444443142
-
The chemokine SDF-1/CXCL12 binds to and signals through the orphan receptor RDC1 in T lymphocytes
-
Balabanian K., Lagane B., Infantino S., Chow K.Y.C., Harriague J., Moepps B., Atenzana-Seisdedos F., Thelen M., Bachelerie F. The chemokine SDF-1/CXCL12 binds to and signals through the orphan receptor RDC1 in T lymphocytes. J. Biol. Chem. 2005, 280:35760-35766.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 35760-35766
-
-
Balabanian, K.1
Lagane, B.2
Infantino, S.3
Chow, K.Y.C.4
Harriague, J.5
Moepps, B.6
Atenzana-Seisdedos, F.7
Thelen, M.8
Bachelerie, F.9
-
267
-
-
77949482428
-
CXCR7 functions as a scavenger for CXCL12 and CXCL11
-
Naumann U., Cameroni E., Pruenster M., Mahabaleshwar H., Raz E., Zerwes H.-G., Tor A., Thelen M. CXCR7 functions as a scavenger for CXCL12 and CXCL11. PLoS One 2010, 5:e9175.
-
(2010)
PLoS One
, vol.5
-
-
Naumann, U.1
Cameroni, E.2
Pruenster, M.3
Mahabaleshwar, H.4
Raz, E.5
Zerwes, H.-G.6
Tor, A.7
Thelen, M.8
-
268
-
-
33645793799
-
Structure modeling of all identified G protein-coupled receptors in the human genome
-
Zhang Y., DeVries M.E., Skolnick J. Structure modeling of all identified G protein-coupled receptors in the human genome. PLoS Comput. Biol. 2006, 2:e13.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Zhang, Y.1
DeVries, M.E.2
Skolnick, J.3
-
269
-
-
33748474838
-
A novel chemokine receptor for SDF-1 and I-TAC involved in cell survival, cell adhesion, and tumor development
-
Burns J.M., Summers B.C., Wang Y., Melikian A., Berahovich R., Miao Z., Penfold M.E.T., Sunshine M.J., Littman D.R., Kuo C.J., Wei K., McMaster B.E., Wright K., Howard M.C., Schall T.J. A novel chemokine receptor for SDF-1 and I-TAC involved in cell survival, cell adhesion, and tumor development. J. Exp. Med. 2006, 203:2201-2213.
-
(2006)
J. Exp. Med.
, vol.203
, pp. 2201-2213
-
-
Burns, J.M.1
Summers, B.C.2
Wang, Y.3
Melikian, A.4
Berahovich, R.5
Miao, Z.6
Penfold, M.E.T.7
Sunshine, M.J.8
Littman, D.R.9
Kuo, C.J.10
Wei, K.11
McMaster, B.E.12
Wright, K.13
Howard, M.C.14
Schall, T.J.15
-
270
-
-
33646881816
-
The orphan G-protein coupled receptor RDC1: evidence for a role in chondrocyte hypertrophy and articular cartilage matrix turnover
-
Jones S.W., Brockbank S.M.V., Mobbs M.L., Le Good N.J., Soma-Haddrick S., Heuze A.J., Langham C.J., Timms D., Newham P., Needham M.R.C. The orphan G-protein coupled receptor RDC1: evidence for a role in chondrocyte hypertrophy and articular cartilage matrix turnover. Osteoarthr. Cartil. 2006, 14:597-608.
-
(2006)
Osteoarthr. Cartil.
, vol.14
, pp. 597-608
-
-
Jones, S.W.1
Brockbank, S.M.V.2
Mobbs, M.L.3
Le Good, N.J.4
Soma-Haddrick, S.5
Heuze, A.J.6
Langham, C.J.7
Timms, D.8
Newham, P.9
Needham, M.R.C.10
-
271
-
-
67149084970
-
The role of histamine H4 receptor in immune and inflammatory disorders
-
Zampeli E., Tiligada E. The role of histamine H4 receptor in immune and inflammatory disorders. Br. J. Pharmacol. 2009, 157:24-33.
-
(2009)
Br. J. Pharmacol.
, vol.157
, pp. 24-33
-
-
Zampeli, E.1
Tiligada, E.2
-
272
-
-
49449111894
-
Delineation of agonist binding to the human histamine H 4 receptor using mutational analysis, homology modeling, and ab initio calculations
-
Jongejan A., Lim H.D., Smits R.A., Haaksma E., Leurs R., For Q., et al. Delineation of agonist binding to the human histamine H 4 receptor using mutational analysis, homology modeling, and ab initio calculations. J. Chem. Inf. Model. 2008, 48:1455-1463.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1455-1463
-
-
Jongejan, A.1
Lim, H.D.2
Smits, R.A.3
Haaksma, E.4
Leurs, R.5
For, Q.6
-
273
-
-
47349116596
-
Activation mechanism of the human histamine H4 receptor - an explicit membrane molecular dynamics simulation study
-
Jójárt B., Kiss R., Viskolcz B., Keseru G.M. Activation mechanism of the human histamine H4 receptor - an explicit membrane molecular dynamics simulation study. J. Chem. Inf. Model. 2008, 48:1199-1210.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 1199-1210
-
-
Jójárt, B.1
Kiss, R.2
Viskolcz, B.3
Keseru, G.M.4
-
274
-
-
67651094164
-
4 receptor
-
4 receptor. ChemMedChem 2009, 4:820-827.
-
(2009)
ChemMedChem
, vol.4
, pp. 820-827
-
-
Tanrikulu, Y.1
Proschak, E.2
Werner, T.3
Geppert, T.4
Todoroff, N.5
Klenner, A.6
Kottke, T.7
Sander, K.8
Schneider, E.9
Seifert, R.10
Stark, H.11
Clark, T.12
Schneider, G.13
-
275
-
-
77956254648
-
4 Receptor and their impact on receptor activation
-
4 Receptor and their impact on receptor activation. Chembiochem 2010, 11:1850-1855.
-
(2010)
Chembiochem
, vol.11
, pp. 1850-1855
-
-
Werner, T.1
Sander, K.2
Tanrikulu, Y.3
Kottke, T.4
Proschak, E.5
Stark, H.6
Schneider, G.7
-
276
-
-
33847323129
-
Epidermal growth factor receptor mutations in lung cancer
-
Sharma S.V., Bell D.W., Settleman J., Haber D.A. Epidermal growth factor receptor mutations in lung cancer. Nat. Rev. Cancer 2007, 7:169-181.
-
(2007)
Nat. Rev. Cancer
, vol.7
, pp. 169-181
-
-
Sharma, S.V.1
Bell, D.W.2
Settleman, J.3
Haber, D.A.4
-
277
-
-
0037013143
-
The conformational plasticity of protein kinases
-
Huse M., Kuriyan J. The conformational plasticity of protein kinases. Cell 2002, 109:275-282.
-
(2002)
Cell
, vol.109
, pp. 275-282
-
-
Huse, M.1
Kuriyan, J.2
-
278
-
-
67549145398
-
Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment
-
Jura N., Endres N.F., Engel K., Deindl S., Das R., Lamers M.H., Wemmer D.E., Zhang X., Kuriyan J. Mechanism for activation of the EGF receptor catalytic domain by the juxtamembrane segment. Cell 2009, 137:1293-1307.
-
(2009)
Cell
, vol.137
, pp. 1293-1307
-
-
Jura, N.1
Endres, N.F.2
Engel, K.3
Deindl, S.4
Das, R.5
Lamers, M.H.6
Wemmer, D.E.7
Zhang, X.8
Kuriyan, J.9
-
279
-
-
33745002702
-
An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
-
Zhang X., Gureasko J., Shen K., Cole P.A., Kuriyan J. An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor. Cell 2006, 125:1137-1149.
-
(2006)
Cell
, vol.125
, pp. 1137-1149
-
-
Zhang, X.1
Gureasko, J.2
Shen, K.3
Cole, P.A.4
Kuriyan, J.5
-
280
-
-
0037291769
-
EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization
-
Ferguson K.M., Berger M.B., Mendrola J.M., Cho H.-S., Leahy D.J., Lemmon M.A. EGF activates its receptor by removing interactions that autoinhibit ectodomain dimerization. Mol. Cell 2003, 11:507-517.
-
(2003)
Mol. Cell
, vol.11
, pp. 507-517
-
-
Ferguson, K.M.1
Berger, M.B.2
Mendrola, J.M.3
Cho, H.-S.4
Leahy, D.J.5
Lemmon, M.A.6
-
281
-
-
18344390418
-
ERBB receptors and cancer: the complexity of targeted inhibitors
-
Hynes N.E., Lane H.A. ERBB receptors and cancer: the complexity of targeted inhibitors. Nat. Rev. Cancer 2005, 5:341-354.
-
(2005)
Nat. Rev. Cancer
, vol.5
, pp. 341-354
-
-
Hynes, N.E.1
Lane, H.A.2
-
282
-
-
69749120935
-
Quantitative prediction of fold resistance for inhibitors of EGFR
-
Balius T.E., Rizzo R.C. Quantitative prediction of fold resistance for inhibitors of EGFR. Biochemistry 2009, 48:8435-8448.
-
(2009)
Biochemistry
, vol.48
, pp. 8435-8448
-
-
Balius, T.E.1
Rizzo, R.C.2
-
283
-
-
79960092299
-
Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs
-
Wan S., Coveney P.V. Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs. J. R. Soc. Interface 2011, 8:1114-1127.
-
(2011)
J. R. Soc. Interface
, vol.8
, pp. 1114-1127
-
-
Wan, S.1
Coveney, P.V.2
-
284
-
-
78649797897
-
Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: a molecular dynamics study
-
Mustafa M., Mirza A., Kannan N. Conformational regulation of the EGFR kinase core by the juxtamembrane and C-terminal tail: a molecular dynamics study. Proteins 2011, 79:99-114.
-
(2011)
Proteins
, vol.79
, pp. 99-114
-
-
Mustafa, M.1
Mirza, A.2
Kannan, N.3
-
285
-
-
67649781716
-
Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics
-
Kästner J., Loeffler H.H., Roberts S.K., Martin-Fernandez M.L., Winn M.D. Ectodomain orientation, conformational plasticity and oligomerization of ErbB1 receptors investigated by molecular dynamics. J. Struct. Biol. 2009, 167:117-128.
-
(2009)
J. Struct. Biol.
, vol.167
, pp. 117-128
-
-
Kästner, J.1
Loeffler, H.H.2
Roberts, S.K.3
Martin-Fernandez, M.L.4
Winn, M.D.5
-
286
-
-
38549132873
-
Single-molecule imaging and fluorescence lifetime imaging microscopy show different structures for high- and low-affinity epidermal growth factor receptors in A431 cells
-
Webb S.E.D., Roberts S.K., Needham S.R., Tynan C.J., Rolfe D.J., Winn M.D., Clarke D.T., Barraclough R. Single-molecule imaging and fluorescence lifetime imaging microscopy show different structures for high- and low-affinity epidermal growth factor receptors in A431 cells. Biophys. J. 2008, 94:803-819.
-
(2008)
Biophys. J.
, vol.94
, pp. 803-819
-
-
Webb, S.E.D.1
Roberts, S.K.2
Needham, S.R.3
Tynan, C.J.4
Rolfe, D.J.5
Winn, M.D.6
Clarke, D.T.7
Barraclough, R.8
-
287
-
-
43149102957
-
The antibody zalutumumab inhibits epidermal growth factor receptor signaling by limiting intra- and intermolecular flexibility
-
Lammerts van Bueren J.J., Bleeker W.K., Brännström A., von Euler A., Jansson M., Peipp M., Schneider-Merck T., Valerius T., van de Winkel J.G.J., Parren P.W.H.I. The antibody zalutumumab inhibits epidermal growth factor receptor signaling by limiting intra- and intermolecular flexibility. Proc. Natl. Acad. Sci. U.S.A. 2008, 105:6109-6114.
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 6109-6114
-
-
Lammerts van Bueren, J.J.1
Bleeker, W.K.2
Brännström, A.3
von Euler, A.4
Jansson, M.5
Peipp, M.6
Schneider-Merck, T.7
Valerius, T.8
van de Winkel, J.G.J.9
Parren, P.W.H.I.10
-
288
-
-
79952937376
-
Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization
-
Zhang Z., Wriggers W. Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization. Biochemistry 2011, 50:2144-2156.
-
(2011)
Biochemistry
, vol.50
, pp. 2144-2156
-
-
Zhang, Z.1
Wriggers, W.2
-
289
-
-
0036258208
-
Cystic fibrosis: a worldwide analysis of CFTR mutations - correlation with incidence data and application to screening
-
Bobadilla J.L., Macek M., Fine J.P., Farrell P.M. Cystic fibrosis: a worldwide analysis of CFTR mutations - correlation with incidence data and application to screening. Hum. Mutat. 2002, 19:575-606.
-
(2002)
Hum. Mutat.
, vol.19
, pp. 575-606
-
-
Bobadilla, J.L.1
Macek, M.2
Fine, J.P.3
Farrell, P.M.4
-
290
-
-
19944432524
-
Impact of the δF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure
-
Lewis H.A., Zhao X., Wang C., Sauder J.M., Rooney I., Noland B.W., Lorimer D., Kearins M.C., Conners K., Condon B., Maloney P.C., Guggino W.B., Hunt J.F., Emtage S. Impact of the δF508 mutation in first nucleotide-binding domain of human cystic fibrosis transmembrane conductance regulator on domain folding and structure. J. Biol. Chem. 2005, 280:1346-1353.
-
(2005)
J. Biol. Chem.
, vol.280
, pp. 1346-1353
-
-
Lewis, H.A.1
Zhao, X.2
Wang, C.3
Sauder, J.M.4
Rooney, I.5
Noland, B.W.6
Lorimer, D.7
Kearins, M.C.8
Conners, K.9
Condon, B.10
Maloney, P.C.11
Guggino, W.B.12
Hunt, J.F.13
Emtage, S.14
-
291
-
-
0031006695
-
Localization and suppression of a kinetic defect in cystic fibrosis transmembrane conductance regulator folding
-
Qu B.H., Strickland E.H., Thomas P.J. Localization and suppression of a kinetic defect in cystic fibrosis transmembrane conductance regulator folding. J. Biol. Chem. 1997, 272:15739-15744.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 15739-15744
-
-
Qu, B.H.1
Strickland, E.H.2
Thomas, P.J.3
-
292
-
-
0029997424
-
Alteration of the cystic fibrosis transmembrane conductance regulator folding pathway
-
Qu B.H., Thomas P.J. Alteration of the cystic fibrosis transmembrane conductance regulator folding pathway. J. Biol. Chem. 1996, 271:7261-7264.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 7261-7264
-
-
Qu, B.H.1
Thomas, P.J.2
-
293
-
-
11444265307
-
Side chain and backbone contributions of Phe508 to CFTR folding
-
Thibodeau P.H., Brautigam C.A., Machius M., Thomas P.J. Side chain and backbone contributions of Phe508 to CFTR folding. Nat. Struct. Mol. Biol. 2005, 12:10-16.
-
(2005)
Nat. Struct. Mol. Biol.
, vol.12
, pp. 10-16
-
-
Thibodeau, P.H.1
Brautigam, C.A.2
Machius, M.3
Thomas, P.J.4
-
294
-
-
40149102264
-
Diminished self-chaperoning activity of the δF508 mutant of CFTR results in protein misfolding
-
Serohijos A.W.R., Hegedus T., Riordan J.R., Dokholyan N.V. Diminished self-chaperoning activity of the δF508 mutant of CFTR results in protein misfolding. PLoS Comput. Biol. 2008, 4:e1000008.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Serohijos, A.W.R.1
Hegedus, T.2
Riordan, J.R.3
Dokholyan, N.V.4
-
295
-
-
77957363101
-
Integrins as therapeutic targets: lessons and opportunities
-
Cox D., Brennan M., Moran N. Integrins as therapeutic targets: lessons and opportunities. Nat. Rev. Drug Discov. 2010, 9:804-820.
-
(2010)
Nat. Rev. Drug Discov.
, vol.9
, pp. 804-820
-
-
Cox, D.1
Brennan, M.2
Moran, N.3
-
296
-
-
0037019269
-
Identification of potent and novel α4β1 antagonists using in silico screening
-
Singh J., van Vlijmen H., Liao Y., Lee W.C., Cornebise M., Harris M., Shu I., Gill A., Cuervo J.H., Abraham W.M., Adams S.P. Identification of potent and novel α4β1 antagonists using in silico screening. J. Med. Chem. 2002, 45:2988-2993.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 2988-2993
-
-
Singh, J.1
van Vlijmen, H.2
Liao, Y.3
Lee, W.C.4
Cornebise, M.5
Harris, M.6
Shu, I.7
Gill, A.8
Cuervo, J.H.9
Abraham, W.M.10
Adams, S.P.11
|