-
1
-
-
66449084442
-
Infrastructure for the life sciences: Design and implementation of the UniProt website
-
Jain, E.; Bairoch, A.; Duvaud, S.; Phan, I.; Redasch, N.; Suzek, B.E.; Martin, M.J.; McGarvey, P.; Gasteiger, E. Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics, 2009, 10, 136.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 136
-
-
Jain, E.1
Bairoch, A.2
Duvaud, S.3
Phan, I.4
Redasch, N.5
Suzek, B.E.6
Martin, M.J.7
McGarvey, P.8
Gasteiger, E.9
-
2
-
-
33745076219
-
Advances in homology protein structure modeling
-
Zhexin, X. Advances in homology protein structure modeling. Curr. Protein. Pept. Sci., 2006, 7(3), 217-227.
-
(2006)
Curr. Protein. Pept. Sci
, vol.7
, Issue.3
, pp. 217-227
-
-
Zhexin, X.1
-
3
-
-
33646002994
-
Comparative modeling for protein structure prediction
-
Ginalski, K. Comparative modeling for protein structure prediction. Curr. Opin. Struct. Biol., 2006, 16(2), 172-177.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, Issue.2
, pp. 172-177
-
-
Ginalski, K.1
-
4
-
-
36749031066
-
Progress from CASP6 to CASP7
-
Kryshtafovych, A.; Fidelis, K.; Moult, J. Progress from CASP6 to CASP7. Proteins, 2007, 69(Suppl 8), 194-207.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 194-207
-
-
Kryshtafovych, A.1
Fidelis, K.2
Moult, J.3
-
5
-
-
44949145113
-
Progress and challenges in protein structure prediction
-
Zhang, Y. Progress and challenges in protein structure prediction. Curr. Opin. Struct. Biol., 2008, 18(3), 342-348.
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, Issue.3
, pp. 342-348
-
-
Zhang, Y.1
-
6
-
-
33744779891
-
Sequence comparison and protein structure prediction
-
Dunbrack, J.R.L. Sequence comparison and protein structure prediction. Curr. Opin. Struct. Biol., 2006, 16(3), 374-384.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, Issue.3
, pp. 374-384
-
-
Dunbrack, J.R.L.1
-
7
-
-
33749991908
-
Comparative protein modeling
-
Esposito, E.X.; Tobi, D.; Madura, J.D. Comparative protein modeling. Rev. Comput. Chem., 2006, 22, 57-167.
-
(2006)
Rev. Comput. Chem
, vol.22
, pp. 57-167
-
-
Esposito, E.X.1
Tobi, D.2
Madura, J.D.3
-
8
-
-
33645972948
-
Servers for protein structure prediction
-
Fischer, D. Servers for protein structure prediction. Curr. Opin. Struct. Biol., 2006, 16(2), 178-182.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, Issue.2
, pp. 178-182
-
-
Fischer, D.1
-
9
-
-
34249824268
-
Computational methods in protein structure prediction
-
Floudas, C.A. Computational methods in protein structure prediction. Biotechnol. Bioeng., 2007, 97(2), 207-213.
-
(2007)
Biotechnol. Bioeng
, vol.97
, Issue.2
, pp. 207-213
-
-
Floudas, C.A.1
-
10
-
-
37149056501
-
A historical perspective of template-based protein structure prediction
-
Guo, J.T.; Ellrott, K.; Xu, Y. A historical perspective of template-based protein structure prediction. Methods Mol. Biol., 2008, 413, 3-42.
-
(2008)
Methods Mol. Biol
, vol.413
, pp. 3-42
-
-
Guo, J.T.1
Ellrott, K.2
Xu, Y.3
-
11
-
-
62849107262
-
Protein structure prediction and model quality assessment
-
Kryshtafovych, A.; Fidelis, K. Protein structure prediction and model quality assessment. Drug Discov. Today, 2009, 14(7-8), 386-393.
-
(2009)
Drug Discov. Today
, vol.14
, Issue.7-8
, pp. 386-393
-
-
Kryshtafovych, A.1
Fidelis, K.2
-
12
-
-
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(5), 1315-1327.
-
(2005)
Protein Sci
, vol.14
, Issue.5
, pp. 1315-1327
-
-
Wallner, B.1
Elofsson, A.2
-
13
-
-
54049091165
-
Sequence based residue depth prediction using evolutionary information and predicted secondary structure
-
Zhang, H.; Zhang, T.; Chen, K.; Shen, S.; Ruan, J.; Kurgan, L. Sequence based residue depth prediction using evolutionary information and predicted secondary structure. BMC Bioinformatics, 2008, 9, 388.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 388
-
-
Zhang, H.1
Zhang, T.2
Chen, K.3
Shen, S.4
Ruan, J.5
Kurgan, L.6
-
14
-
-
20444484434
-
A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
-
Moult, J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr. Opin. Struct. Biol., 2005, 15(3), 285-289.
-
(2005)
Curr. Opin. Struct. Biol
, vol.15
, Issue.3
, pp. 285-289
-
-
Moult, J.1
-
15
-
-
36749103110
-
Automated server predictions in CASP7
-
Battey, J.N.; 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.1
Kopp, J.2
Bordoli, L.3
Read, R.J.4
Clarke, N.D.5
Schwede, T.6
-
16
-
-
74249097379
-
CASP8 results in context of previous experiments
-
Kryshtafovych, A.; Fidelis, K.; Moult, J. CASP8 results in context of previous experiments. Proteins, 2009, 77 (Suppl 9),217-228.
-
(2009)
Proteins
, vol.77
, Issue.SUPPL. 9
, pp. 217-228
-
-
Kryshtafovych, A.1
Fidelis, K.2
Moult, J.3
-
17
-
-
0025183708
-
Basic Local Alignment Search Tool
-
Altschul, S.F.; Gish, W.; Miller, W.; Myers, E.W.; Lipman, D.J. Basic Local Alignment Search Tool. J. Mol. Biol., 1990, 215(3), 403-410.
-
(1990)
J. Mol. Biol
, vol.215
, Issue.3
, pp. 403-410
-
-
Altschul, S.F.1
Gish, W.2
Miller, W.3
Myers, E.W.4
Lipman, D.J.5
-
18
-
-
0025950944
-
Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms
-
Pearson, W.R. Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics, 1991, 11(3), 635-650.
-
(1991)
Genomics
, vol.11
, Issue.3
, pp. 635-650
-
-
Pearson, W.R.1
-
19
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F.; Madden, T.L.; Schaffer, A.A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 1997, 25(17), 3389-3402.
-
(1997)
Nucleic Acids Res
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
20
-
-
0031743421
-
Profile hidden Markov models
-
Eddy, S.R. Profile hidden Markov models. Bioinformatics, 1998, 14(9), 755-763.
-
(1998)
Bioinformatics
, vol.14
, Issue.9
, pp. 755-763
-
-
Eddy, S.R.1
-
21
-
-
38549141229
-
Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre
-
Bennett-Lovsey, R.M.; Herbert, A.D.; Sternberg, M.J.; Kelley, L.A. Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre. Proteins, 2008, 70(3), 611-625.
-
(2008)
Proteins
, vol.70
, Issue.3
, pp. 611-625
-
-
Bennett-Lovsey, R.M.1
Herbert, A.D.2
Sternberg, M.J.3
Kelley, L.A.4
-
22
-
-
58149088781
-
-
Agarwal, V.; Remmert, M.; Biegert, A.; Söding, J. PDBalert: Automatic, recurrent remote homology tracking and protein structure prediction. BMC Struct. Biol., 2008, 8, 51.
-
Agarwal, V.; Remmert, M.; Biegert, A.; Söding, J. PDBalert: Automatic, recurrent remote homology tracking and protein structure prediction. BMC Struct. Biol., 2008, 8, 51.
-
-
-
-
23
-
-
16344373015
-
Protein homology detection by HMM-HMM comparison
-
Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics, 2005, 21(7), 951-960.
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 951-960
-
-
Soding, J.1
-
24
-
-
34447506573
-
Fold recognition by concurrent use of solvent accessibility and residue depth
-
Liu, S.; Zhang, C.; Liang, S.; Zhou, Y. Fold recognition by concurrent use of solvent accessibility and residue depth. Proteins, 2007, 68(3), 636-645.
-
(2007)
Proteins
, vol.68
, Issue.3
, pp. 636-645
-
-
Liu, S.1
Zhang, C.2
Liang, S.3
Zhou, Y.4
-
25
-
-
48449085801
-
SP5: Improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model
-
Zhang, W.; Liu, S.; Zhou, Y. SP5: improving protein fold recognition by using torsion angle profiles and profile-based gap penalty model. PLoS One, 2008, 3(6), e2325.
-
(2008)
PLoS One
, vol.3
, Issue.6
-
-
Zhang, W.1
Liu, S.2
Zhou, Y.3
-
26
-
-
33745616114
-
A machine learning information retrieval approach to protein fold recognition
-
Cheng, J.; Baldi, P. A machine learning information retrieval approach to protein fold recognition. Bioinformatics, 2006, 22(12), 1456-1463.
-
(2006)
Bioinformatics
, vol.22
, Issue.12
, pp. 1456-1463
-
-
Cheng, J.1
Baldi, P.2
-
27
-
-
34547569522
-
COMPASS server for remote homology inference
-
Web Server issue, W653-658
-
Sadreyev, R.I.; Tang, M.; Kim, B.H.; Grishin, N.V. COMPASS server for remote homology inference. Nucleic Acids Res., 2007, 35(Web Server issue), W653-658.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Sadreyev, R.I.1
Tang, M.2
Kim, B.H.3
Grishin, N.V.4
-
28
-
-
32144458563
-
Application of latent semantic analysis to protein remote homology detection
-
Dong, Q.W.; Wang, X.L.; Lin, L. Application of latent semantic analysis to protein remote homology detection. Bioinformatics, 2006, 22(3), 285-290.
-
(2006)
Bioinformatics
, vol.22
, Issue.3
, pp. 285-290
-
-
Dong, Q.W.1
Wang, X.L.2
Lin, L.3
-
29
-
-
33846947543
-
Motif kernel generated by genetic programming improves remote homology and fold detection
-
Hådstad, T.; Hestnes, A.J.H.; Saetrom, P. Motif kernel generated by genetic programming improves remote homology and fold detection. BMC Bioinformatics, 2007, 8, 23.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 23
-
-
Hådstad, T.1
Hestnes, A.J.H.2
Saetrom, P.3
-
30
-
-
33644843469
-
On single and multiple models of protein families for the detection of remote sequence relationships
-
Casbon, J.A.; Saqi, M.A. On single and multiple models of protein families for the detection of remote sequence relationships. BMC Bioinformatics, 2006, 7, 48.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 48
-
-
Casbon, J.A.1
Saqi, M.A.2
-
31
-
-
34547871261
-
Fast model-based protein homology detection without alignment
-
Hochreiter, S.; Heusel, M.; Obermayer, K. Fast model-based protein homology detection without alignment. Bioinformatics, 2007, 23(14), 1728-1736.
-
(2007)
Bioinformatics
, vol.23
, Issue.14
, pp. 1728-1736
-
-
Hochreiter, S.1
Heusel, M.2
Obermayer, K.3
-
32
-
-
46049106732
-
Word correlation matrices for protein sequence analysis and remote homology detection
-
Lingner, T.; Meinicke, P. Word correlation matrices for protein sequence analysis and remote homology detection. BMC Bioinformatics, 2008, 9, 259.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 259
-
-
Lingner, T.1
Meinicke, P.2
-
33
-
-
58149345703
-
A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis
-
Liu, B.; Wang, X.; Lin, L.; Dong, Q. A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis. BMC Bioinformatics, 2008, 9, 510.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 510
-
-
Liu, B.1
Wang, X.2
Lin, L.3
Dong, Q.4
-
34
-
-
33747843430
-
HHsenser: Exhaustive transitive profile search using HMM-HMM comparison
-
Web Server issue, W374-378
-
Söding, J.; Remmert, M.; Biegert, A.; Lupas, A.N. HHsenser: exhaustive transitive profile search using HMM-HMM comparison. Nucleic Acids Res., 2006, 34(Web Server issue), W374-378.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Söding, J.1
Remmert, M.2
Biegert, A.3
Lupas, A.N.4
-
35
-
-
41149118582
-
Protein structure mining using a structural alphabet
-
Tyagi, M.; de Brevern, A.G.; Srinivasan, N.; Offmann, B. Protein structure mining using a structural alphabet. Proteins, 2008, 71(2), 920-937.
-
(2008)
Proteins
, vol.71
, Issue.2
, pp. 920-937
-
-
Tyagi, M.1
de Brevern, A.G.2
Srinivasan, N.3
Offmann, B.4
-
36
-
-
34447648188
-
-
Melvin, I.; Ie, E.; Kuang, R.; Weston, J.; Stafford, W.N.; Leslie, C. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinformatics, 2007, 8(Suppl), 4, S2.
-
Melvin, I.; Ie, E.; Kuang, R.; Weston, J.; Stafford, W.N.; Leslie, C. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition. BMC Bioinformatics, 2007, 8(Suppl), 4, S2.
-
-
-
-
37
-
-
43349094032
-
Probabilistic multi-class multikernel learning: On protein fold recognition and remote homology detection
-
Damoulas, T.; Girolami, M.A. Probabilistic multi-class multikernel learning: on protein fold recognition and remote homology detection. Bioinformatics, 2008, 24(10), 1264-1270.
-
(2008)
Bioinformatics
, vol.24
, Issue.10
, pp. 1264-1270
-
-
Damoulas, T.1
Girolami, M.A.2
-
38
-
-
33746333850
-
SVM-based detection of distant protein structural relationships using pairwise probabilistic suffix trees
-
Oǧul, H.; Mumcuoǧlu, E.U. SVM-based detection of distant protein structural relationships using pairwise probabilistic suffix trees. Comput. Biol. Chem., 2006, 30(4), 292-299.
-
(2006)
Comput. Biol. Chem
, vol.30
, Issue.4
, pp. 292-299
-
-
Oǧul, H.1
Mumcuoǧlu, E.U.2
-
39
-
-
33747854648
-
-
Bhadra, R.; Sandhya, S.; Abhinandan, K.R.; Chakrabarti, S.; Sowdhamini, R.; Srinivasan, N. Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. Nucleic Acids Res., 2006, 34(Web Server issue), W143-146.
-
Bhadra, R.; Sandhya, S.; Abhinandan, K.R.; Chakrabarti, S.; Sowdhamini, R.; Srinivasan, N. Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. Nucleic Acids Res., 2006, 34(Web Server issue), W143-146.
-
-
-
-
40
-
-
34250674964
-
The WWWH of remote homolog detection: The state of the art
-
Fariselli, P.; Rossi, I.; Capriotti, E.; Casadio, R. The WWWH of remote homolog detection: the state of the art. Brief Bioinform., 2007, 8(2), 78-87.
-
(2007)
Brief Bioinform
, vol.8
, Issue.2
, pp. 78-87
-
-
Fariselli, P.1
Rossi, I.2
Capriotti, E.3
Casadio, R.4
-
41
-
-
85142150204
-
-
Becker, E.; Cotillard, A.; Meyer, V.; Madaoui, H.; Guérois, R. HMM-Kalign: a tool for generating sub-optimal HMM alignments. Bioinformatics, 2007, 23(22), 3095-3097.
-
Becker, E.; Cotillard, A.; Meyer, V.; Madaoui, H.; Guérois, R. HMM-Kalign: a tool for generating sub-optimal HMM alignments. Bioinformatics, 2007, 23(22), 3095-3097.
-
-
-
-
42
-
-
47249098645
-
Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection
-
Jung, I.; Lee, J.; Lee, S.Y.; Kim, D. Application of nonnegative matrix factorization to improve profile-profile alignment features for fold recognition and remote homolog detection. BMC Bioinformatics, 2008, 9, 298.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 298
-
-
Jung, I.1
Lee, J.2
Lee, S.Y.3
Kim, D.4
-
43
-
-
39449089407
-
Improving model construction of profile HMMs for remote homology detection through structural alignment
-
Bernardes, J.S.; Dávila, A.M.; Costa, V.S.; Zaverucha, G. Improving model construction of profile HMMs for remote homology detection through structural alignment. BMC Bioinformatics, 2007, 8, 435.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 435
-
-
Bernardes, J.S.1
Dávila, A.M.2
Costa, V.S.3
Zaverucha, G.4
-
44
-
-
33746239564
-
Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences
-
Tan, Y.H.; Huang, H.; Kihara, D. Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences. Proteins, 2006, 64(3), 587-600.
-
(2006)
Proteins
, vol.64
, Issue.3
, pp. 587-600
-
-
Tan, Y.H.1
Huang, H.2
Kihara, D.3
-
45
-
-
0033967524
-
Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: Application to the human procarboxypeptidase A2
-
Aloy, P.; Mas, J.M.; Marti-Renom, M.A.; Querol, E.; Aviles, F.X.; Oliva, B. Refinement of modelled structures by knowledge-based energy profiles and secondary structure prediction: application to the human procarboxypeptidase A2. J. Comput. Aided Mol. Des., 2000, 14(1), 83-92.
-
(2000)
J. Comput. Aided Mol. Des
, vol.14
, Issue.1
, pp. 83-92
-
-
Aloy, P.1
Mas, J.M.2
Marti-Renom, M.A.3
Querol, E.4
Aviles, F.X.5
Oliva, B.6
-
46
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom, M.A.; Stuart, A.C.; Fiser, A.; Sanchez, R.; Melo, F.; Sali, A. Comparative protein structure modeling of genes and genomes. Ann. Rev. Biophys. Biomol. Struct., 2000, 29, 291-325.
-
(2000)
Ann. Rev. Biophys. Biomol. Struct
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.C.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
47
-
-
33751108305
-
A Consensus Data Mining secondary structure prediction by combining GOR V and fragment database mining
-
Sen, T.Z.; Cheng, H.; Kloczkowski, A.; Jernigan, R.L. A Consensus Data Mining secondary structure prediction by combining GOR V and fragment database mining. Protein Sci., 2006, 15(11), 2499-2506.
-
(2006)
Protein Sci
, vol.15
, Issue.11
, pp. 2499-2506
-
-
Sen, T.Z.1
Cheng, H.2
Kloczkowski, A.3
Jernigan, R.L.4
-
48
-
-
0034334542
-
Computational methods for protein secondary structure prediction using multiple sequence alignments
-
Heringa, J. Computational methods for protein secondary structure prediction using multiple sequence alignments. Curr. Protein Pept. Sci., 2000, 1(3), 273-301.
-
(2000)
Curr. Protein Pept. Sci
, vol.1
, Issue.3
, pp. 273-301
-
-
Heringa, J.1
-
49
-
-
34547127137
-
Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information
-
Pollastri, G.; Martin, A.J.; Mooney, C.; Vullo, A. Accurate prediction of protein secondary structure and solvent accessibility by consensus combiners of sequence and structure information. BMC Bioinformatics, 2007, 8, 201.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 201
-
-
Pollastri, G.1
Martin, A.J.2
Mooney, C.3
Vullo, A.4
-
50
-
-
33747586510
-
Improving the accuracy of protein secondary structure prediction using structural alignment
-
Montgomerie, S.; Sundararaj, S.; Gallin, W.J.; Wishart, D.S. Improving the accuracy of protein secondary structure prediction using structural alignment. BMC Bioinformatics, 2006, 7, 301.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 301
-
-
Montgomerie, S.1
Sundararaj, S.2
Gallin, W.J.3
Wishart, D.S.4
-
51
-
-
35748978197
-
Consensus data mining (CDM) Protein Secondary Structure Prediction Server: Combining GOR V and Fragment Database Mining (FDM)
-
Cheng, H.; Sen, T.Z.; Jernigan, R.L.; Kloczkowski, A. Consensus data mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM). Bioinformatics, 2007, 23(19), 2628-2630.
-
(2007)
Bioinformatics
, vol.23
, Issue.19
, pp. 2628-2630
-
-
Cheng, H.1
Sen, T.Z.2
Jernigan, R.L.3
Kloczkowski, A.4
-
52
-
-
48449106792
-
The Jpred 3 secondary structure prediction server
-
Web Server issue, W197-W201
-
Cole, C.; Barber, J.D.; Barton, G.J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res., 2008, 36(Web Server issue), W197-W201.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Cole, C.1
Barber, J.D.2
Barton, G.J.3
-
53
-
-
33846249595
-
MUPRED: A tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction
-
Bondugula, R.; Xu, D. MUPRED: a tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction. Proteins, 2007, 66(3), 664-670.
-
(2007)
Proteins
, vol.66
, Issue.3
, pp. 664-670
-
-
Bondugula, R.1
Xu, D.2
-
54
-
-
33746267388
-
YASSPP: Better kernels and coding schemes lead to improvements in protein secondary structure prediction
-
Karypis, G. YASSPP: better kernels and coding schemes lead to improvements in protein secondary structure prediction. Proteins, 2006, 64(3), 575-586.
-
(2006)
Proteins
, vol.64
, Issue.3
, pp. 575-586
-
-
Karypis, G.1
-
55
-
-
25144432549
-
HYPROSP II - a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence
-
Lin, H.N.; Chang, J.M.; Wu, K.P.; Sung, T.Y.; Hsu, W.L. HYPROSP II - a knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence. Bioinformatics, 2005, 21(15), 3227-3233.
-
(2005)
Bioinformatics
, vol.21
, Issue.15
, pp. 3227-3233
-
-
Lin, H.N.1
Chang, J.M.2
Wu, K.P.3
Sung, T.Y.4
Hsu, W.L.5
-
56
-
-
40549143077
-
A dynamic Bayesian network approach to protein secondary structure prediction
-
Yao, X.Q.; Zhu, H.; She, Z.S. A dynamic Bayesian network approach to protein secondary structure prediction. BMC Bioinformatics, 2008, 9, 49.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 49
-
-
Yao, X.Q.1
Zhu, H.2
She, Z.S.3
-
57
-
-
33745259286
-
Protein secondary structure prediction for a single-sequence using hidden semimarkov models
-
Aydin, Z.; Altunbasak, Y.; Borodovsky, M. Protein secondary structure prediction for a single-sequence using hidden semimarkov models. BMC Bioinformatics, 2006, 7, 178.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 178
-
-
Aydin, Z.1
Altunbasak, Y.2
Borodovsky, M.3
-
58
-
-
55949118135
-
A protein secondary structure prediction framework based on the Extreme Learning Machine
-
Wang, G.R.; Zhao, Y.; Wang, D. A protein secondary structure prediction framework based on the Extreme Learning Machine. Neurocomputing, 2008, 72(1-3), 262-268.
-
(2008)
Neurocomputing
, vol.72
, Issue.1-3
, pp. 262-268
-
-
Wang, G.R.1
Zhao, Y.2
Wang, D.3
-
59
-
-
77949390712
-
-
Rost, B. Rising accuracy of protein secondary structure prediction In: Protein Structure Determination, Analysis, and Modeling for Drug Discovery. Chasman, D., Ed.; Dekker: New York, 2003, pp. 207-249.
-
Rost, B. Rising accuracy of protein secondary structure prediction In: Protein Structure Determination, Analysis, and Modeling for Drug Discovery. Chasman, D., Ed.; Dekker: New York, 2003, pp. 207-249.
-
-
-
-
60
-
-
85142181677
-
-
Pollastri, G.; McLysaght, A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics, 2005, 21(8), 1719-1720.
-
Pollastri, G.; McLysaght, A. Porter: a new, accurate server for protein secondary structure prediction. Bioinformatics, 2005, 21(8), 1719-1720.
-
-
-
-
61
-
-
36049007258
-
An evolutionary method for learning HMM structure: Prediction of protein secondary structure
-
Won, K.J.; Hamelryck, T.; Prügel-Bennett, A.; Krogh, A. An evolutionary method for learning HMM structure: prediction of protein secondary structure. BMC Bioinformatics, 2007, 8, 357.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 357
-
-
Won, K.J.1
Hamelryck, T.2
Prügel-Bennett, A.3
Krogh, A.4
-
62
-
-
50049099447
-
Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures
-
Duan, M.; Huang, M.; Ma, C.; Li, L.; Zhou, Y. Position-specific residue preference features around the ends of helices and strands and a novel strategy for the prediction of secondary structures. Protein Sci., 2008, 17(9), 1505-1512.
-
(2008)
Protein Sci
, vol.17
, Issue.9
, pp. 1505-1512
-
-
Duan, M.1
Huang, M.2
Ma, C.3
Li, L.4
Zhou, Y.5
-
63
-
-
38049047106
-
Prediction of Protein Secondary Structure with two-stage multi-class SVMs
-
Nguyen, M.N.; Rajapakse, J.C. Prediction of Protein Secondary Structure with two-stage multi-class SVMs. Int. J. Data Min. Bioinform., 2007, 1(3), 248-269.
-
(2007)
Int. J. Data Min. Bioinform
, vol.1
, Issue.3
, pp. 248-269
-
-
Nguyen, M.N.1
Rajapakse, J.C.2
-
64
-
-
0027136282
-
Comparative Protein Modeling by Satisfaction of Spatial Restraints
-
Sali, A.; Blundell, T.L. Comparative Protein Modeling by Satisfaction of Spatial Restraints. J. Mol. Biol., 1993, 234(3), 779-815.
-
(1993)
J. Mol. Biol
, vol.234
, Issue.3
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
65
-
-
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(2), 507-533.
-
(1992)
J. Mol. Biol
, vol.226
, Issue.2
, pp. 507-533
-
-
Levitt, M.1
-
66
-
-
0022531028
-
The predicted structure of immunoglobulin-D1.3 and its comparison with the crystal-structure
-
Chothia, C.; Lesk, A.M.; Levitt, M.; Amit, A.G.; Mariuzza, R.A.; Phillips, S.E.V.; Poljak, R.J. The predicted structure of immunoglobulin-D1.3 and its comparison with the crystal-structure. Science, 1986, 233(4765), 755-758.
-
(1986)
Science
, vol.233
, Issue.4765
, pp. 755-758
-
-
Chothia, C.1
Lesk, A.M.2
Levitt, M.3
Amit, A.G.4
Mariuzza, R.A.5
Phillips, S.E.V.6
Poljak, R.J.7
-
67
-
-
0023305986
-
Knowledge-based prediction of protein structures and the design of novel molecules
-
Blundell, T.L.; Sibanda, B.L.; Sternberg, M.J.E.; Thornton, J.M. Knowledge-based prediction of protein structures and the design of novel molecules. Nature, 1987, 326(6111), 347-352.
-
(1987)
Nature
, vol.326
, Issue.6111
, pp. 347-352
-
-
Blundell, T.L.1
Sibanda, B.L.2
Sternberg, M.J.E.3
Thornton, J.M.4
-
68
-
-
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.; 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.11
Alexov, E.12
Honig, B.13
-
69
-
-
44349091007
-
Using multiple templates to improve quality of homology models in automated homology modeling
-
Larsson, P.; Wallner, B.; Lindahl, E.; Elofsson, A. Using multiple templates to improve quality of homology models in automated homology modeling. Protein Sci., 2008, 17(6), 990-1002.
-
(2008)
Protein Sci
, vol.17
, Issue.6
, pp. 990-1002
-
-
Larsson, P.1
Wallner, B.2
Lindahl, E.3
Elofsson, A.4
-
70
-
-
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. Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins, 2001, (Suppl 5), 39-46.
-
(2001)
Proteins
, Issue.SUPPL. 5
, pp. 39-46
-
-
Bates, P.A.1
Kelley, L.A.2
MacCallum, R.M.3
Sternberg, M.J.4
-
71
-
-
0042622380
-
SWISS-MODEL: An automated protein homology-modeling server
-
Schwede, T.; Kopp, J.; Guex, N.; Peitsch, M.C. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 2003, 31(13), 3381-3385.
-
(2003)
Nucleic Acids Res
, vol.31
, Issue.13
, pp. 3381-3385
-
-
Schwede, T.1
Kopp, J.2
Guex, N.3
Peitsch, M.C.4
-
72
-
-
77949379118
-
-
1010 Sherbrooke Street West, 910, Montreal, Quebec, Canada H3A 2R7
-
Chemical Computing Group Inc. Molecular Operating Environment, 2004.03, 1010 Sherbrooke Street West, #910, Montreal, Quebec, Canada H3A 2R7, 2004.
-
(2004)
Chemical Computing Group Inc. Molecular Operating Environment, 2004.03
-
-
-
73
-
-
36749061828
-
Template-based modeling and free modeling by ITASSER in CASP7
-
Zhang, Y. Template-based modeling and free modeling by ITASSER in CASP7. Proteins, 2007, 69(Suppl 8), 108-117.
-
(2007)
Proteins
, vol.69
, Issue.SUPPL. 8
, pp. 108-117
-
-
Zhang, Y.1
-
74
-
-
39449115394
-
-
Zhang, Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 2008, 9, 40.
-
Zhang, Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, 2008, 9, 40.
-
-
-
-
75
-
-
34547612652
-
Pcons.net: Protein structure prediction meta server
-
Web Server issue, W369-374
-
Wallner, B.; Larsson, P.; Elofsson, A. Pcons.net: protein structure prediction meta server. Nucleic Acids Res., 2007, 35(Web Server issue), W369-374.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Wallner, B.1
Larsson, P.2
Elofsson, A.3
-
76
-
-
10744230917
-
Automated prediction of CASP-5 structures using the Robetta server
-
Chivian, D.; Kim, D.E.; Malmström, L.; Bradley, P.; Robertson, T.; Murphy, P.; Strauss, C.E.; Bonneau, R.; Rohl, C.A.; Baker, D. Automated prediction of CASP-5 structures using the Robetta server. Proteins, 2003, 53(Suppl 6), 524-533.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 524-533
-
-
Chivian, D.1
Kim, D.E.2
Malmström, L.3
Bradley, P.4
Robertson, T.5
Murphy, P.6
Strauss, C.E.7
Bonneau, R.8
Rohl, C.A.9
Baker, D.10
-
77
-
-
33845365051
-
-
Pandit, S.B.; Zhang, Y.; Skolnick, J. TASSER-Lite: An automated tool for protein comparative modeling. Biophys. J., 2006, 91(11), 4180-4190.
-
Pandit, S.B.; Zhang, Y.; Skolnick, J. TASSER-Lite: An automated tool for protein comparative modeling. Biophys. J., 2006, 91(11), 4180-4190.
-
-
-
-
78
-
-
34547574147
-
M4T: A comparative protein structure modeling server
-
Web Server issue, W363-368
-
Fernandez-Fuentes, N.; Madrid-Aliste, C.J.; Rai, B.K.; Fajardo, J.E.; Fiser, A. M4T: a comparative protein structure modeling server. Nucleic Acids Res., 2007, 35(Web Server issue), W363-368.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Fernandez-Fuentes, N.1
Madrid-Aliste, C.J.2
Rai, B.K.3
Fajardo, J.E.4
Fiser, A.5
-
79
-
-
48449093089
-
-
Montgomerie, S.; Cruz, J.A.; Shrivastava, S.; Arndt, D.; Berjanskii, M.; Wishart, D.S. PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res., 2008, 36(Web Server issue), W202-209.
-
Montgomerie, S.; Cruz, J.A.; Shrivastava, S.; Arndt, D.; Berjanskii, M.; Wishart, D.S. PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res., 2008, 36(Web Server issue), W202-209.
-
-
-
-
80
-
-
24644439203
-
Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops
-
Fernandez-Fuentes, N.; Querol, E.; Aviles, F.X.; Sternberg, M.J.E.; Oliva, B. Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops. Proteins, 2005, 60(4), 746-757.
-
(2005)
Proteins
, vol.60
, Issue.4
, pp. 746-757
-
-
Fernandez-Fuentes, N.1
Querol, E.2
Aviles, F.X.3
Sternberg, M.J.E.4
Oliva, B.5
-
81
-
-
47349128896
-
Toward better refinement of comparative models: Predicting loops in inexact environments
-
Sellers, B.D.; Zhu, K.; Zhao, S.; Friesner, R.A.; Jacobson, M.P. Toward better refinement of comparative models: Predicting loops in inexact environments. Proteins, 2008, 72(3), 959-971.
-
(2008)
Proteins
, vol.72
, Issue.3
, pp. 959-971
-
-
Sellers, B.D.1
Zhu, K.2
Zhao, S.3
Friesner, R.A.4
Jacobson, M.P.5
-
82
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser, A.; Do, R.K.G.; Sali, A. Modeling of loops in protein structures. Protein Sci., 2000, 9(9), 1753-1773.
-
(2000)
Protein Sci
, vol.9
, Issue.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.G.2
Sali, A.3
-
83
-
-
38549154569
-
Loop modeling: Sampling, filtering, and scoring
-
Soto, C.S.; Fasnacht, M.; Zhu, J.; Forrest, L.; Honig, B. Loop modeling: Sampling, filtering, and scoring. Proteins, 2008, 70(3), 834-843.
-
(2008)
Proteins
, vol.70
, Issue.3
, pp. 834-843
-
-
Soto, C.S.1
Fasnacht, M.2
Zhu, J.3
Forrest, L.4
Honig, B.5
-
84
-
-
36448975211
-
Modeling protein loops with knowledge-based prediction of sequence-structure alignment
-
Peng, H.P.; Yang, A.S. Modeling protein loops with knowledge-based prediction of sequence-structure alignment. Bioinformatics, 2007, 23(21), 2836-2842.
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2836-2842
-
-
Peng, H.P.1
Yang, A.S.2
-
85
-
-
0347899425
-
-
Espadaler, J.; Fernandez-Fuentes, N.; Hermoso, A.; Querol, E.; Aviles, F.X.; Sternberg, M.J.; Oliva, B. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res., 2004, 32(Database issue), D185-188.
-
Espadaler, J.; Fernandez-Fuentes, N.; Hermoso, A.; Querol, E.; Aviles, F.X.; Sternberg, M.J.; Oliva, B. ArchDB: automated protein loop classification as a tool for structural genomics. Nucleic Acids Res., 2004, 32(Database issue), D185-188.
-
-
-
-
86
-
-
33747863016
-
-
Fernandez-Fuentes, N.; Zhai, J.; Fiser, A. ArchPRED: a template based loop structure prediction server. Nucleic Acids Res., 2006, 34(Web Server issue), W173-176.
-
Fernandez-Fuentes, N.; Zhai, J.; Fiser, A. ArchPRED: a template based loop structure prediction server. Nucleic Acids Res., 2006, 34(Web Server issue), W173-176.
-
-
-
-
87
-
-
43149093569
-
Protein loop modeling using fragment assembly
-
Lee, D.S.; Seok, C.; Lee, J. Protein loop modeling using fragment assembly. J. Korean Phys. Soc., 2008, 52(4), 1137-1142.
-
(2008)
J. Korean Phys. Soc
, vol.52
, Issue.4
, pp. 1137-1142
-
-
Lee, D.S.1
Seok, C.2
Lee, J.3
-
88
-
-
1842532008
-
A hierarchical approach to all-atom protein loop prediction
-
Jacobson, M.P.; Pincus, D.L.; Rapp, C.S.; Day, T.J.; Honig, B.; Shaw, D.E.; Friesner, R.A. A hierarchical approach to all-atom protein loop prediction. Proteins, 2004, 55(2), 351-367.
-
(2004)
Proteins
, vol.55
, Issue.2
, pp. 351-367
-
-
Jacobson, M.P.1
Pincus, D.L.2
Rapp, C.S.3
Day, T.J.4
Honig, B.5
Shaw, D.E.6
Friesner, R.A.7
-
89
-
-
56549099908
-
Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field
-
Cui, M.; Mezei, M.; Osman, R. Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field. Protein Eng. Des. Sel., 2008, 21(12), 729-735.
-
(2008)
Protein Eng. Des. Sel
, vol.21
, Issue.12
, pp. 729-735
-
-
Cui, M.1
Mezei, M.2
Osman, R.3
-
90
-
-
58149157667
-
Prediction of protein loop conformations using the AGBNP implicit solvent model and torsion angle sampling
-
Felts, A.K.; Gallicchio, E.; Chekmarev, D.; Paris, K.A.; Friesner, R.A.; Levy, R.M. Prediction of protein loop conformations using the AGBNP implicit solvent model and torsion angle sampling. J. Chem. Theory Comput., 2008, 4(5), 855-868.
-
(2008)
J. Chem. Theory Comput
, vol.4
, Issue.5
, pp. 855-868
-
-
Felts, A.K.1
Gallicchio, E.2
Chekmarev, D.3
Paris, K.A.4
Friesner, R.A.5
Levy, R.M.6
-
91
-
-
0037188507
-
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
-
Xiang, Z.X.; Soto, C.S.; Honig, B. Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction. Proc. Natl. Acad. Sci. USA, 2002, 99(11), 7432-7437.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, Issue.11
, pp. 7432-7437
-
-
Xiang, Z.X.1
Soto, C.S.2
Honig, B.3
-
92
-
-
40549088876
-
Prediction of protein loop conformations using multiscale Modeling methods with physical energy scoring functions
-
Olson, M.A.; Feig, M.; Brooks, C.L. Prediction of protein loop conformations using multiscale Modeling methods with physical energy scoring functions. J. Comput. Chem., 2008, 29(5), 820-831.
-
(2008)
J. Comput. Chem
, vol.29
, Issue.5
, pp. 820-831
-
-
Olson, M.A.1
Feig, M.2
Brooks, C.L.3
-
93
-
-
33748988479
-
Long loop prediction using the protein local optimization program
-
Zhu, K.; Pincus, D.L.; Zhao, S.W.; Friesner, R.A. Long loop prediction using the protein local optimization program. Proteins, 2006, 65(2), 438-452.
-
(2006)
Proteins
, vol.65
, Issue.2
, pp. 438-452
-
-
Zhu, K.1
Pincus, D.L.2
Zhao, S.W.3
Friesner, R.A.4
-
94
-
-
39749085824
-
LOOPER: A molecular mechanics-based algorithm for protein loop prediction
-
Spassov, V.Z.; Flook, P.K.; Yan, L. LOOPER: a molecular mechanics-based algorithm for protein loop prediction. Protein Eng. Des. Sel., 2008, 21(2), 91-100.
-
(2008)
Protein Eng. Des. Sel
, vol.21
, Issue.2
, pp. 91-100
-
-
Spassov, V.Z.1
Flook, P.K.2
Yan, L.3
-
95
-
-
36649014061
-
Improved methods for side chain and loop predictions via the protein local optimization program: Variable dielectric model for implicitly improving the treatment of polarization effects
-
Zhu, K.; Shirts, M.R.; Friesner, R.A. Improved methods for side chain and loop predictions via the protein local optimization program: Variable dielectric model for implicitly improving the treatment of polarization effects. J. Chem. Theory Comput., 2007, 3(6), 2108-2119.
-
(2007)
J. Chem. Theory Comput
, vol.3
, Issue.6
, pp. 2108-2119
-
-
Zhu, K.1
Shirts, M.R.2
Friesner, R.A.3
-
97
-
-
77949365757
-
-
Al-Lazikani, B, Jung, J, Xiang, Z, Honig, B. Protein Structure
-
Al-Lazikani, B.; Jung, J.; Xiang, Z.; Honig, B. Protein Structure
-
-
-
-
98
-
-
77949405440
-
-
Prediction
-
Prediction. Curr. Opin. Chem. Biol., 2001, 5(1), 51-56.
-
(2001)
Curr. Opin. Chem. Biol
, vol.5
, Issue.1
, pp. 51-56
-
-
-
99
-
-
51349094337
-
Minimizing and learning energy functions for side-chain prediction
-
Yanover, C.; Schueler-Furman, O.; Weiss, Y. Minimizing and learning energy functions for side-chain prediction. J. Comput. Biol., 2008, 15(7), 899-911.
-
(2008)
J. Comput. Biol
, vol.15
, Issue.7
, pp. 899-911
-
-
Yanover, C.1
Schueler-Furman, O.2
Weiss, Y.3
-
100
-
-
50049116635
-
A fast and accurate method for side-chain modeling
-
Lu, M.Y.; Dousis, A.D.; Ma, J.P. OPUS-Rota: A fast and accurate method for side-chain modeling. Protein Sci., 2008, 17(9), 1576-1585.
-
(2008)
Protein Sci
, vol.17
, Issue.9
, pp. 1576-1585
-
-
Lu, M.Y.1
Dousis, A.D.2
Ma3
OPUS-Rota, J.P.4
-
101
-
-
31544455877
-
Grow to Fit Molecular Dynamics (G2FMD): An ab initio method for protein side-chain assignment and refinement
-
Zhang, W.; Duan, Y. Grow to Fit Molecular Dynamics (G2FMD): an ab initio method for protein side-chain assignment and refinement. Protein Eng. Des. Sel., 2006, 19(2), 55-65.
-
(2006)
Protein Eng. Des. Sel
, vol.19
, Issue.2
, pp. 55-65
-
-
Zhang, W.1
Duan, Y.2
-
102
-
-
36248992483
-
Prediction of side chain Orientations in proteins by statistical machine learning methods
-
Yan, A.; Kloczkowski, A.; Hofmann, H.; Jernigan, R.L. Prediction of side chain Orientations in proteins by statistical machine learning methods. J. Biomol. Struct. Dyn., 2007, 25(3), 275-287.
-
(2007)
J. Biomol. Struct. Dyn
, vol.25
, Issue.3
, pp. 275-287
-
-
Yan, A.1
Kloczkowski, A.2
Hofmann, H.3
Jernigan, R.L.4
-
103
-
-
0042511005
-
A graph-theory algorithm for rapid protein side-chain prediction
-
Canutescu, A.A.; Shelenkov, A.A.; Dunbrack, R.L. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci., 2003, 12(9), 2001-2014.
-
(2003)
Protein Sci
, vol.12
, Issue.9
, pp. 2001-2014
-
-
Canutescu, A.A.1
Shelenkov, A.A.2
Dunbrack, R.L.3
-
104
-
-
34250792960
-
A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models
-
Hartmann, C.; Antes, I.; Lengauer, T. IRECS: A new algorithm for the selection of most probable ensembles of side-chain conformations in protein models. Protein Sci., 2007, 16(7), 1294-1307.
-
(2007)
Protein Sci
, vol.16
, Issue.7
, pp. 1294-1307
-
-
Hartmann, C.1
Antes, I.2
Lengauer3
IRECS, T.4
-
105
-
-
33847261239
-
The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions
-
Spassov, V.Z.; Yan, L.; Flook, P.K. The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions. Protein Sci., 2007, 16(3), 494-506.
-
(2007)
Protein Sci
, vol.16
, Issue.3
, pp. 494-506
-
-
Spassov, V.Z.1
Yan, L.2
Flook, P.K.3
-
106
-
-
32144439339
-
Residue-rotamer-reduction algorithm for the protein side-chain conformation problem
-
Xie, W.; Sahinidis, N.V. Residue-rotamer-reduction algorithm for the protein side-chain conformation problem. Bioinformatics, 2006, 22(2), 188-194.
-
(2006)
Bioinformatics
, vol.22
, Issue.2
, pp. 188-194
-
-
Xie, W.1
Sahinidis, N.V.2
-
107
-
-
33846603216
-
High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design
-
Dantas, G.; Corrent, C.; Reichow, S.L.; Havranek, J.J.; Eletr, Z.M.; Isern, N.G.; Kuhlman, B.; Varani, G.; Merritt, E.A.; Baker, D. High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. J. Mol. Bio., 2007, 366(4), 1209-1221.
-
(2007)
J. Mol. Bio
, vol.366
, Issue.4
, pp. 1209-1221
-
-
Dantas, G.1
Corrent, C.2
Reichow, S.L.3
Havranek, J.J.4
Eletr, Z.M.5
Isern, N.G.6
Kuhlman, B.7
Varani, G.8
Merritt, E.A.9
Baker, D.10
-
108
-
-
34248586877
-
Computational sidechain placement and protein mutagenesis with implicit solvent models
-
Lopes, A.; Alexandrov, A.; Bathelt, C.; Archontis, G.; Simonson, T. Computational sidechain placement and protein mutagenesis with implicit solvent models. Proteins, 2007, 67(4), 853-867.
-
(2007)
Proteins
, vol.67
, Issue.4
, pp. 853-867
-
-
Lopes, A.1
Alexandrov, A.2
Bathelt, C.3
Archontis, G.4
Simonson, T.5
-
109
-
-
39149099199
-
The ModFOLD server for the quality assessment of protein structural models
-
McGuffin, L.J. The ModFOLD server for the quality assessment of protein structural models. Bioinformatics, 2008, 24(4), 586-587.
-
(2008)
Bioinformatics
, vol.24
, Issue.4
, pp. 586-587
-
-
McGuffin, L.J.1
-
110
-
-
46749143822
-
FragQA: Predicting local fragment quality of a sequence-structure alignment
-
Gao, X.; Bu, D.; Li, S.C.; Xu, J.; Li, M. FragQA: predicting local fragment quality of a sequence-structure alignment. Genome Inform., 2007, 19, 27-39.
-
(2007)
Genome Inform
, vol.19
, pp. 27-39
-
-
Gao, X.1
Bu, D.2
Li, S.C.3
Xu, J.4
Li, M.5
-
111
-
-
33645504195
-
Identification of correct regions in protein models using structural, alignment, and consensus information
-
Wallner, B.; Elofsson, A. Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci., 2006, 15(4), 900-913.
-
(2006)
Protein Sci
, vol.15
, Issue.4
, pp. 900-913
-
-
Wallner, B.1
Elofsson, A.2
-
112
-
-
41549086671
-
Validation of protein models by a neural network approach
-
Mereghetti, P.; Ganadu, M.L.; Papaleo, E.; Fantucci, P.; De Gioia, L. Validation of protein models by a neural network approach. BMC Bioinformatics, 2008, 9, 66.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 66
-
-
Mereghetti, P.1
Ganadu, M.L.2
Papaleo, E.3
Fantucci, P.4
De Gioia, L.5
-
113
-
-
34547566446
-
ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
-
Web Server issue, W407-410
-
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(Web Server issue), W407-410.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Wiederstein, M.1
Sippl, M.J.2
-
114
-
-
40549141792
-
A comprehensive scoring function for model quality assessment
-
Benkert, P.; Tosatto, S.C.; Schomburg, D. QMEAN: A comprehensive scoring function for model quality assessment. Proteins, 2008, 71(1), 261-277.
-
(2008)
Proteins
, vol.71
, Issue.1
, pp. 261-277
-
-
Benkert, P.1
Tosatto, S.C.2
Schomburg3
QMEAN, D.4
-
115
-
-
33745726716
-
A composite score for predicting errors in protein structure models
-
Eramian, D.; Shen, M.Y.; Devos, D.; Melo, F.; Sali, A.; Marti-Renom, M.A. A composite score for predicting errors in protein structure models. Protein Sci., 2006, 15(7), 1653-1666.
-
(2006)
Protein Sci
, vol.15
, Issue.7
, pp. 1653-1666
-
-
Eramian, D.1
Shen, M.Y.2
Devos, D.3
Melo, F.4
Sali, A.5
Marti-Renom, M.A.6
-
116
-
-
42449122271
-
Ranking predicted protein structures with support vector regression
-
Qiu, J.; Sheffler, W.; Baker, D.; Noble, W.S. Ranking predicted protein structures with support vector regression. Proteins, 2008, 71(3), 1175-1182.
-
(2008)
Proteins
, vol.71
, Issue.3
, pp. 1175-1182
-
-
Qiu, J.1
Sheffler, W.2
Baker, D.3
Noble, W.S.4
-
117
-
-
62849113729
-
SELECTpro: Effective protein model selection using a structure-based energy function resistant to BLUNDERs
-
Randall, A.; Baldi, P. SELECTpro: effective protein model selection using a structure-based energy function resistant to BLUNDERs. BMC Struct. Biol., 2008, 8(1), 52.
-
(2008)
BMC Struct. Biol
, vol.8
, Issue.1
, pp. 52
-
-
Randall, A.1
Baldi, P.2
-
118
-
-
0242362161
-
Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
-
Karplus, K.; Karchin, R.; Draper, J.; Casper, J.; Mandel-Gutfreund, Y.; Diekhans, M.; Hughey, R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins, 2003, 53(Suppl 6), 491-496.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 491-496
-
-
Karplus, K.1
Karchin, R.2
Draper, J.3
Casper, J.4
Mandel-Gutfreund, Y.5
Diekhans, M.6
Hughey, R.7
-
119
-
-
66149084059
-
Model quality assessment using distance constraints from alignments
-
Paluszewski, M.; Karplus, K. Model quality assessment using distance constraints from alignments. Proteins, 2009, 75(3), 540-549.
-
(2009)
Proteins
, vol.75
, Issue.3
, pp. 540-549
-
-
Paluszewski, M.1
Karplus, K.2
-
120
-
-
33947203766
-
Evaluation of the structural quality of modeled proteins by using globularity criteria
-
Costantini, S.; Facchiano, A.M.; Colonna, G. Evaluation of the structural quality of modeled proteins by using globularity criteria. BMC Struct. Biol., 2007, 7, 9.
-
(2007)
BMC Struct. Biol
, vol.7
, pp. 9
-
-
Costantini, S.1
Facchiano, A.M.2
Colonna, G.3
-
121
-
-
35648988945
-
Benchmarking consensus model quality assessment for protein fold recognition
-
McGuffin, L.J. Benchmarking consensus model quality assessment for protein fold recognition. BMC Bioinformatics, 2007, 8, 345.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 345
-
-
McGuffin, L.J.1
-
122
-
-
24144437430
-
Improving sequence-based fold recognition by using 3D model quality assessment
-
Pettitt, C.S.; McGuffin, L.J.; Jones, D.T. Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics, 2005, 21(17), 3509-3515.
-
(2005)
Bioinformatics
, vol.21
, Issue.17
, pp. 3509-3515
-
-
Pettitt, C.S.1
McGuffin, L.J.2
Jones, D.T.3
-
123
-
-
0242299169
-
Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller
-
Wallner, B.; Fang, H.; Elofsson, A. Automatic consensus-based fold recognition using Pcons, ProQ, and Pmodeller. Proteins, 2003, 53(Suppl 6), 534-541.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 534-541
-
-
Wallner, B.1
Fang, H.2
Elofsson, A.3
-
124
-
-
33749572252
-
Minimalist representations and the importance of nearest neighbor effects in protein folding simulations
-
Colubri, A.; Jha, A.K.; Shen, M.Y.; Sali, A.; Berry, R.S.; Sosnick, T.R.; Freed, K.F. Minimalist representations and the importance of nearest neighbor effects in protein folding simulations. J. Mol. Biol., 2006, 363(4), 835-857.
-
(2006)
J. Mol. Biol
, vol.363
, Issue.4
, pp. 835-857
-
-
Colubri, A.1
Jha, A.K.2
Shen, M.Y.3
Sali, A.4
Berry, R.S.5
Sosnick, T.R.6
Freed, K.F.7
-
125
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
Shen, M.Y.; Sali, A. Statistical potential for assessment and prediction of protein structures. Protein Sci., 2006, 15(11), 2507-2524.
-
(2006)
Protein Sci
, vol.15
, Issue.11
, pp. 2507-2524
-
-
Shen, M.Y.1
Sali, A.2
-
126
-
-
28144448406
-
The victor/FRST function for model quality estimation
-
Tosatto, S.C. The victor/FRST function for model quality estimation. J. Comput. Biol., 2005, 12(10), 1316-1327.
-
(2005)
J. Comput. Biol
, vol.12
, Issue.10
, pp. 1316-1327
-
-
Tosatto, S.C.1
-
127
-
-
66149156968
-
Evaluating the absolute quality of a single protein model using structural features and support vector machines
-
Wang, Z.; Tegge, A.N.; Cheng, J. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins, 2008, 75(3), 638-647.
-
(2008)
Proteins
, vol.75
, Issue.3
, pp. 638-647
-
-
Wang, Z.1
Tegge, A.N.2
Cheng, J.3
-
128
-
-
42449119311
-
Protein model quality assessment prediction by combining fragment comparisons and a consensus C(α) contact potential
-
Zhou, H.; Skolnick, J. Protein model quality assessment prediction by combining fragment comparisons and a consensus C(α) contact potential. Proteins, 2008, 71(3), 1211-1218.
-
(2008)
Proteins
, vol.71
, Issue.3
, pp. 1211-1218
-
-
Zhou, H.1
Skolnick, J.2
-
129
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
Zhou, H.Y.; Zhou, Y.Q. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci., 2002, 11(11), 2714-2726.
-
(2002)
Protein Sci
, vol.11
, Issue.11
, pp. 2714-2726
-
-
Zhou, H.Y.1
Zhou, Y.Q.2
-
130
-
-
34547576789
-
Local quality assessment in homology models using statistical potentials and support vector machines
-
Fasnacht, M.; Zhu, J.; Honig, B. Local quality assessment in homology models using statistical potentials and support vector machines. Protein Sci., 2007, 16(8), 1557-1568.
-
(2007)
Protein Sci
, vol.16
, Issue.8
, pp. 1557-1568
-
-
Fasnacht, M.1
Zhu, J.2
Honig, B.3
-
131
-
-
42449093288
-
Estimating quality of template-based protein models by alignment stability
-
Chen, H.; Kihara, D. Estimating quality of template-based protein models by alignment stability. Proteins, 2008, 71(3), 1255-1274.
-
(2008)
Proteins
, vol.71
, Issue.3
, pp. 1255-1274
-
-
Chen, H.1
Kihara, D.2
-
132
-
-
36749027045
-
-
Terashi, G.; Takeda-Shitaka, M.; Kanou, K.; Iwadate, M.; Takaya, D.; Hosoi, A.; Ohta, K.; Umeyama, H. Fams-ace: a combined method to select the best model after remodeling all server models. Proteins, 2007, 69(Suppl 8), 98-107.
-
Terashi, G.; Takeda-Shitaka, M.; Kanou, K.; Iwadate, M.; Takaya, D.; Hosoi, A.; Ohta, K.; Umeyama, H. Fams-ace: a combined method to select the best model after remodeling all server models. Proteins, 2007, 69(Suppl 8), 98-107.
-
-
-
-
133
-
-
54949097750
-
-
Pawlowski, M.; Gajda, M.J.; Matlak, R.; Bujnicki, J.M. MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics, 2008, 9, 403.
-
Pawlowski, M.; Gajda, M.J.; Matlak, R.; Bujnicki, J.M. MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics, 2008, 9, 403.
-
-
-
-
134
-
-
66149136906
-
Applying undertaker cost functions to model quality assessment
-
Archie, J.; Karplus, K. Applying undertaker cost functions to model quality assessment. Proteins, 2009, 75(3), 550-555.
-
(2009)
Proteins
, vol.75
, Issue.3
, pp. 550-555
-
-
Archie, J.1
Karplus, K.2
-
135
-
-
67649518035
-
Homology modeling in drug discovery: Current trends and applications
-
Cavasotto, C.N.; Phatak, S.S. Homology modeling in drug discovery: current trends and applications. Drug Discov. Today, 2009, 14(13-14), 676-683.
-
(2009)
Drug Discov. Today
, vol.14
, Issue.13-14
, pp. 676-683
-
-
Cavasotto, C.N.1
Phatak, S.S.2
-
136
-
-
68149144249
-
Discovery of novel inhibitors of Streptococcus pneumoniae based on the virtual screening with the homology-modeled structure of histidine kinase (VicK)
-
Li, N.; Wang, F.; Niu, S.; Cao, J.; Wu, K.; Li, Y.; Yin, N.; Zhang, X.; Zhu, W.; Yin, Y. Discovery of novel inhibitors of Streptococcus pneumoniae based on the virtual screening with the homology-modeled structure of histidine kinase (VicK). BMC Microbiol., 2009, 9, 129.
-
(2009)
BMC Microbiol
, vol.9
, pp. 129
-
-
Li, N.1
Wang, F.2
Niu, S.3
Cao, J.4
Wu, K.5
Li, Y.6
Yin, N.7
Zhang, X.8
Zhu, W.9
Yin, Y.10
-
137
-
-
66449109839
-
Carbonic anhydrase inhibitors. Inhibition and homology modeling studies of the fungal β-carbonic anhydrase from Candida albicans with sulfonamides
-
Innocenti, A.; Hall, R.A.; Schlicker, C.; Scozzafava, A.; Steegborn, C.; Mühlschlegel, F.A.; Supuran, C.T. Carbonic anhydrase inhibitors. Inhibition and homology modeling studies of the fungal β-carbonic anhydrase from Candida albicans with sulfonamides. Bioorg. Med. Chem., 2009, 17(13), 4503-4509.
-
(2009)
Bioorg. Med. Chem
, vol.17
, Issue.13
, pp. 4503-4509
-
-
Innocenti, A.1
Hall, R.A.2
Schlicker, C.3
Scozzafava, A.4
Steegborn, C.5
Mühlschlegel, F.A.6
Supuran, C.T.7
-
138
-
-
67349134721
-
A comparative analysis of binding sites between mouse CYP2C38 and CYP2C39 based on homology modeling, molecular dynamics simulation and docking studies
-
Meng, X.-Y.; Zheng, Q.-C.; Zhang, H.-X. A comparative analysis of binding sites between mouse CYP2C38 and CYP2C39 based on homology modeling, molecular dynamics simulation and docking studies. Biochim. Biophys. Acta, 2009, 1794(7), 1066-1072.
-
(2009)
Biochim. Biophys. Acta
, vol.1794
, Issue.7
, pp. 1066-1072
-
-
Meng, X.-Y.1
Zheng, Q.-C.2
Zhang, H.-X.3
-
139
-
-
56349134321
-
Understanding the molecular basis of HBV drug resistance by molecular modeling
-
Sharon, A.; Chu, C.K. Understanding the molecular basis of HBV drug resistance by molecular modeling. Antiviral Res., 2008, 80(3), 339-353.
-
(2008)
Antiviral Res
, vol.80
, Issue.3
, pp. 339-353
-
-
Sharon, A.1
Chu, C.K.2
-
140
-
-
45749124056
-
Homology modeling and site-directed mutagenesis to identify selective inhibitors of endothelin-converting enzyme-2
-
Gagnidze, K.; Sachchidanand; Rozenfeld, R.; Mezei, M.; Zhou, M.-M.; Devi, L.A. Homology modeling and site-directed mutagenesis to identify selective inhibitors of endothelin-converting enzyme-2. J. Med. Chem., 2008, 51(12), 3378-3387.
-
(2008)
J. Med. Chem
, vol.51
, Issue.12
, pp. 3378-3387
-
-
Gagnidze, K.1
Sachchidanand2
Rozenfeld, R.3
Mezei, M.4
Zhou, M.-M.5
Devi, L.A.6
-
141
-
-
44949168495
-
Discovery of novel human histamine H4 receptor ligands by large-scale structure-based virtual screening
-
Kiss, R.; Kiss, B.; Könczöl, A.; 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(11), 3145-3153.
-
(2008)
J. Med. Chem
, vol.51
, Issue.11
, pp. 3145-3153
-
-
Kiss, R.1
Kiss, B.2
Könczöl, A.3
Szalai, F.4
Jelinek, I.5
László, V.6
Noszál, B.7
Falus, A.8
Keseru, G.M.9
-
142
-
-
33751086742
-
Ligand-supported homology modeling of the human angiotensin II type 1 (AT(1)) receptor: Insights into the molecular determinants of telmisartan binding
-
Patny, A.; Desai, P.V.; Avery, M.A. Ligand-supported homology modeling of the human angiotensin II type 1 (AT(1)) receptor: insights into the molecular determinants of telmisartan binding. Proteins, 2006, 65(4), 824-842.
-
(2006)
Proteins
, vol.65
, Issue.4
, pp. 824-842
-
-
Patny, A.1
Desai, P.V.2
Avery, M.A.3
-
143
-
-
13944255377
-
Structure-based drug discovery using GPCR homology modeling: Successful virtual screening for antagonists of the alpha1A adrenergic receptor
-
Evers, A.; Klabunde, T. Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alpha1A adrenergic receptor. J. Med. Chem., 2005, 48(4), 1088-1097.
-
(2005)
J. Med. Chem
, vol.48
, Issue.4
, pp. 1088-1097
-
-
Evers, A.1
Klabunde, T.2
-
144
-
-
68149095775
-
Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics
-
Ekonomiuk, D.; Su, X.C.; Ozawa, K.; Bodenreider, C.; Lim, S.P.; Otting, G.; Huang, D.; Caflisch, A. Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics. J. Med. Chem., 2009, 52(15), 4860-4868.
-
(2009)
J. Med. Chem
, vol.52
, Issue.15
, pp. 4860-4868
-
-
Ekonomiuk, D.1
Su, X.C.2
Ozawa, K.3
Bodenreider, C.4
Lim, S.P.5
Otting, G.6
Huang, D.7
Caflisch, A.8
-
145
-
-
57349106476
-
Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: A combined approach of molecular dynamics and ligand docking
-
Hritz, J.; de Ruiter, A.; Oostenbrink, C. Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking. J. Med. Chem., 2008, 51(23), 7469-7477.
-
(2008)
J. Med. Chem
, vol.51
, Issue.23
, pp. 7469-7477
-
-
Hritz, J.1
de Ruiter, A.2
Oostenbrink, C.3
-
146
-
-
65249120827
-
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes
-
Rueda, M.; Bottegoni, G.; Abagyan, R. Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J. Chem. Inf. Model, 2009, 49(3), 716-725.
-
(2009)
J. Chem. Inf. Model
, vol.49
, Issue.3
, pp. 716-725
-
-
Rueda, M.1
Bottegoni, G.2
Abagyan, R.3
-
147
-
-
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.; 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., Jr. 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(3), 581-588.
-
(2008)
J. Med. Chem
, vol.51
, Issue.3
, pp. 581-588
-
-
Cavasotto, C.N.1
Orry, A.J.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 Jr., F.J.13
-
148
-
-
30444455296
-
Homology modeling of the serotonin 5-HT1A receptor using automated docking of bioactive compounds with defined geometry
-
Nowak, M.; Kolaczkowski, M.; Pawlowski, M.; Bojarski, A.J. Homology modeling of the serotonin 5-HT1A receptor using automated docking of bioactive compounds with defined geometry. J. Med. Chem., 2006, 49(1), 205-214.
-
(2006)
J. Med. Chem
, vol.49
, Issue.1
, pp. 205-214
-
-
Nowak, M.1
Kolaczkowski, M.2
Pawlowski, M.3
Bojarski, A.J.4
-
149
-
-
56349095598
-
SCWRL and MolIDE: Computer programs for side-chain conformation prediction and homology modeling
-
Wang, Q.; Canutescu, A.A.; Dunbrack, R.L., Jr. SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling. Nat. Protoc., 2008, 3(12), 1832-1847.
-
(2008)
Nat. Protoc
, vol.3
, Issue.12
, pp. 1832-1847
-
-
Wang, Q.1
Canutescu, A.A.2
Dunbrack Jr., R.L.3
-
150
-
-
33845462136
-
Side chain placement using estimation of distribution algorithms
-
Santana, R.; Larranaga, P.; Lozano, J.A. Side chain placement using estimation of distribution algorithms. Artif. Intell. Med., 2007, 39(1), 49-63.
-
(2007)
Artif. Intell. Med
, vol.39
, Issue.1
, pp. 49-63
-
-
Santana, R.1
Larranaga, P.2
Lozano, J.A.3
-
151
-
-
33748207212
-
Configurational-bias sampling technique for predicting side-chain conformations in proteins
-
Jain, T.; Cerutti, D.S.; McCammon, J.A. Configurational-bias sampling technique for predicting side-chain conformations in proteins. Protein Sci., 2006, 15(9), 2029-2039.
-
(2006)
Protein Sci
, vol.15
, Issue.9
, pp. 2029-2039
-
-
Jain, T.1
Cerutti, D.S.2
McCammon, J.A.3
-
152
-
-
3242887695
-
Protein structure prediction and analysis using the Robetta server
-
Kim, D.E.; Chivian, D.; Baker, D. Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res., 2004, 32(Suppl. 2), W526-531.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.SUPPL. 2
-
-
Kim, D.E.1
Chivian, D.2
Baker, D.3
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