-
1
-
-
3242884966
-
High-throughput docking as a source of novel drug leads
-
DOI 10.1016/j.cbpa.2004.05.001, PII S1367593104000729
-
JC Alvarez 2004 High-throughput docking as a source of novel drug leads Curr Opin Chem Biol 8 365 370 1:CAS:528:DC%2BD2cXmt1Omsrw%3D 10.1016/j.cbpa.2004.05.001 (Pubitemid 38993729)
-
(2004)
Current Opinion in Chemical Biology
, vol.8
, Issue.4
, pp. 365-370
-
-
Alvarez, J.C.1
-
2
-
-
0038748179
-
Virtual Screening of Virtual Libraries
-
DOI 10.1016/S0079-6468(02)41002-8, PII S0079646802410028
-
DV Green 2003 Virtual screening of virtual libraries Prog Med Chem 41 61 97 1:CAS:528:DC%2BD3sXkt1GntrY%3D 10.1016/S0079-6468(02)41002-8 (Pubitemid 137639533)
-
(2003)
Progress in Medicinal Chemistry
, vol.41
, pp. 61-97
-
-
Green, D.V.S.1
-
3
-
-
0034130384
-
Molecular modeling and computer aided drug design. Examples of their applications in medicinal chemistry
-
1:CAS:528:DC%2BD3cXht12rsLs%3D
-
F Ooms 2000 Molecular modeling and computer aided drug design. Examples of their applications in medicinal chemistry Curr Med Chem 7 141 158 1:CAS:528:DC%2BD3cXht12rsLs%3D
-
(2000)
Curr Med Chem
, vol.7
, pp. 141-158
-
-
Ooms, F.1
-
4
-
-
30744469769
-
From in vivo to in vitro/in silico ADME: Progress and challenges
-
10.1517/17425255.1.1.1
-
H van de Waterbeemd 2005 From in vivo to in vitro/in silico ADME: progress and challenges Expert Opin Drug Metab Toxicol 1 1 4 10.1517/17425255.1.1.1
-
(2005)
Expert Opin Drug Metab Toxicol
, vol.1
, pp. 1-4
-
-
Van De Waterbeemd, H.1
-
5
-
-
76149120388
-
Software news and update AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
1:CAS:528:DC%2BD1MXhsFGnur3O
-
O Trott AJ Olson 2010 Software news and update AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading J Comput Chem 31 455 461 1:CAS:528: DC%2BD1MXhsFGnur3O
-
(2010)
J Comput Chem
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
6
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-
1:CAS:528:DC%2BD1MXht1GitrnK 10.1002/jcc.21256
-
GM Morris R Huey W Lindstrom MF Sanner RK Belew DS Goodsell AJ Olson 2009 AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility J Comput Chem 30 2785 2791 1:CAS:528:DC%2BD1MXht1GitrnK 10.1002/jcc.21256
-
(2009)
J Comput Chem
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
Belew, R.K.5
Goodsell, D.S.6
Olson, A.J.7
-
7
-
-
23444454552
-
The Amber biomolecular simulation programs
-
DOI 10.1002/jcc.20290
-
DA Case TE Cheatham T Darden H Gohlke R Luo KM Merz A Onufriev C Simmerling B Wang RJ Woods 2005 The Amber biomolecular simulation programs J Comput Chem 26 1668 1688 1:CAS:528:DC%2BD2MXht1SlsbbM 10.1002/jcc.20290 (Pubitemid 43076180)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.16
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
8
-
-
77951215074
-
New computational method for prediction of interacting protein loop regions
-
1:CAS:528:DC%2BC3cXks1Kgs7k%3D
-
ML Danielson MA Lill 2010 New computational method for prediction of interacting protein loop regions Proteins 78 1748 1759 1:CAS:528: DC%2BC3cXks1Kgs7k%3D
-
(2010)
Proteins
, vol.78
, pp. 1748-1759
-
-
Danielson, M.L.1
Lill, M.A.2
-
9
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced and scalable molecular simulation
-
1:CAS:528:DC%2BD1cXhsVSqurc%3D 10.1021/ct700301q
-
B Hess C Kutzner D van der Spoel E Lindahl 2008 GROMACS 4: Algorithms for highly efficient, load-balanced and scalable molecular simulation J Chem Theory Comput 4 435 447 1:CAS:528:DC%2BD1cXhsVSqurc%3D 10.1021/ct700301q
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
10
-
-
0029633186
-
Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
-
1:CAS:528:DyaK2MXps1Wrtrw%3D 10.1016/0010-4655(95)00041-D
-
DA Pearlman DA Case JW Caldwell WS Ross TE Cheatham S Debolt D Ferguson G Seibel P Kollman 1995 Amber, a package of computer-programs for applying molecular mechanics, normal-mode analysis molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules Comput Phys Commun 91 1 41 1:CAS:528:DyaK2MXps1Wrtrw%3D 10.1016/0010-4655(95) 00041-D
-
(1995)
Comput Phys Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
11
-
-
77953325845
-
Ligand docking and binding site analysis with PyMOL and Autodock/Vina
-
1:CAS:528:DC%2BC3cXntVahtLo%3D 10.1007/s10822-010-9352-6
-
D Seeliger BL de Groot 2010 Ligand docking and binding site analysis with PyMOL and Autodock/Vina J Comput Aided Mol Des 24 417 422 1:CAS:528: DC%2BC3cXntVahtLo%3D 10.1007/s10822-010-9352-6
-
(2010)
J Comput Aided Mol des
, vol.24
, pp. 417-422
-
-
Seeliger, D.1
De Groot, B.L.2
-
12
-
-
38549154569
-
Loop modeling: Sampling, filtering, and scoring
-
DOI 10.1002/prot.21612
-
CS Soto M Fasnacht J Zhu L Forrest B Honig 2008 Loop modeling: sampling, filtering, and scoring Proteins 70 834 843 1:CAS:528:DC%2BD1cXhvF2ntLY%3D 10.1002/prot.21612 (Pubitemid 351161942)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.3
, pp. 834-843
-
-
Soto, C.S.1
Fasnacht, M.2
Zhu, J.3
Forrest, L.4
Honig, B.5
-
13
-
-
0038174853
-
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, snd virtual screening
-
DOI 10.1023/A:1023866311551
-
MI Zavodszky PC Sanschagrin RS Korde LA Kuhn 2002 Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening J Comput Aided Mol Des 16 883 902 1:CAS:528:DC%2BD3sXjvFyjtLo%3D 10.1023/A:1023866311551 (Pubitemid 36701524)
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.12
, pp. 883-902
-
-
Zavodsky, M.I.1
Sanschagrin, P.C.2
Korde, R.S.3
Kuhn, L.A.4
-
14
-
-
68949190585
-
Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity
-
10.1007/s00894-009-0468-3
-
FA de Molfetta RF de Freitas AB da Silva CA Montanari 2009 Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity J Mol Model 15 1175 1184 10.1007/s00894-009-0468-3
-
(2009)
J Mol Model
, vol.15
, pp. 1175-1184
-
-
De Molfetta, F.A.1
De Freitas, R.F.2
Da Silva, A.B.3
Montanari, C.A.4
-
15
-
-
40649101151
-
Rescoring docking hit lists for model cavity sites: Predictions and experimental testing
-
1:CAS:528:DC%2BD1cXjsVSltL0%3D 10.1016/j.jmb.2008.01.049
-
AP Graves DM Shivakumar SE Boyce MP Jacobson DA Case BK Shoichet 2008 Rescoring docking hit lists for model cavity sites: predictions and experimental testing J Mol Biol 377 914 934 1:CAS:528:DC%2BD1cXjsVSltL0%3D 10.1016/j.jmb.2008.01.049
-
(2008)
J Mol Biol
, vol.377
, pp. 914-934
-
-
Graves, A.P.1
Shivakumar, D.M.2
Boyce, S.E.3
Jacobson, M.P.4
Case, D.A.5
Shoichet, B.K.6
-
16
-
-
33744783960
-
A combination of docking/dynamics simulations and pharmacophoric modeling to discover new dual c-Src/Abl kinase inhibitors
-
DOI 10.1021/jm060236z
-
F Manetti GA Locatelli G Maga S Schenone M Modugno S Forli F Corelli M Botta 2006 A combination of docking/dynamics simulations and pharmacophoric modeling to discover new dual c-Src/Abl kinase inhibitors J Med Chem 49 3278 3286 1:CAS:528:DC%2BD28XktFeiu7o%3D 10.1021/jm060236z (Pubitemid 43830525)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.11
, pp. 3278-3286
-
-
Manetti, F.1
Locatelli, G.A.2
Maga, G.3
Schenone, S.4
Modugno, M.5
Forli, S.6
Corelli, F.7
Botta, M.8
-
17
-
-
73349093728
-
High-performance drug discovery: Computational screening by combining docking and molecular dynamics simulations
-
10.1371/journal.pcbi.1000528
-
N Okimoto N Futatsugi H Fuji A Suenaga G Morimoto R Yanai Y Ohno T Narumi M Taiji 2009 High-performance drug discovery: computational screening by combining docking and molecular dynamics simulations PLoS Comput Biol 5 e1000528 10.1371/journal.pcbi.1000528
-
(2009)
PLoS Comput Biol
, vol.5
, pp. 1000528
-
-
Okimoto, N.1
Futatsugi, N.2
Fuji, H.3
Suenaga, A.4
Morimoto, G.5
Yanai, R.6
Ohno, Y.7
Narumi, T.8
Taiji, M.9
-
18
-
-
73349111930
-
Scoring ensembles of docked protein:ligand interactions for virtual lead optimization
-
1:CAS:528:DC%2BD1MXhsV2nurzI 10.1021/ci9003078
-
JL Paulsen AC Anderson 2009 Scoring ensembles of docked protein:ligand interactions for virtual lead optimization J Chem Inf Model 49 2813 2819 1:CAS:528:DC%2BD1MXhsV2nurzI 10.1021/ci9003078
-
(2009)
J Chem Inf Model
, vol.49
, pp. 2813-2819
-
-
Paulsen, J.L.1
Anderson, A.C.2
-
19
-
-
77951131275
-
Dynamic ligand-induced-fit simulation via enhanced conformational samplings and ensemble dockings: A survivin example
-
1:CAS:528:DC%2BC3cXjvVKnt7w%3D 10.1021/jp911085d
-
IH Park C Li 2010 Dynamic ligand-induced-fit simulation via enhanced conformational samplings and ensemble dockings: a survivin example J. Phys. Chem. B 114 5144 5153 1:CAS:528:DC%2BC3cXjvVKnt7w%3D 10.1021/jp911085d
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 5144-5153
-
-
Park, I.H.1
Li, C.2
-
20
-
-
57349106476
-
Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: A combined approach of molecular dynamics and ligand docking
-
1:CAS:528:DC%2BD1cXhtlGrsr%2FO 10.1021/jm801005m
-
J Hritz A de Ruiter C Ostenbrink 2008 Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking J Med Chem 51 7469 7477 1:CAS:528:DC%2BD1cXhtlGrsr%2FO 10.1021/jm801005m
-
(2008)
J Med Chem
, vol.51
, pp. 7469-7477
-
-
Hritz, J.1
De Ruiter, A.2
Ostenbrink, C.3
-
21
-
-
33846036096
-
The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
-
DOI 10.1093/nar/gkl971
-
H Berman K Henrick H Nakamura JL Markley 2007 The worldwide Protein Data Bank (wwPDB): ensuring a single uniform archive of PDB data Nucleic Acids Res 35 D301 D303 1:CAS:528:DC%2BD2sXivFKmtQ%3D%3D 10.1093/nar/gkl971 (Pubitemid 46056219)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
Markley, J.L.4
-
22
-
-
0033954256
-
The protein data bank
-
1:CAS:528:DC%2BD3cXhvVKjt7w%3D 10.1093/nar/28.1.235
-
HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne 2000 The protein data bank Nucleic Acids Res 28 235 242 1:CAS:528:DC%2BD3cXhvVKjt7w%3D 10.1093/nar/28.1.235
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
23
-
-
0033614004
-
Asparagine and glutamine: Using hydrogen atom contacts in the choice of side-chain amide orientation
-
DOI 10.1006/jmbi.1998.2401
-
JM Word SC Lovell JS Richardson DC Richardson 1999 Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation J Mol Biol 285 1735 1747 1:CAS:528:DyaK1MXhtV2ht7g%3D 10.1006/jmbi.1998.2401 (Pubitemid 29060467)
-
(1999)
Journal of Molecular Biology
, vol.285
, Issue.4
, pp. 1735-1747
-
-
Word, J.M.1
Lovell, S.C.2
Richardson, J.S.3
Richardson, D.C.4
-
24
-
-
33745599120
-
NQ-Flipper: Validation and correction of asparagine/glutamine amide rotamers in protein crystal structures
-
DOI 10.1093/bioinformatics/btl128
-
CX Weichenberger MJ Sippl 2006 NQ-Flipper: validation and correction of asparagine/glutamine amide rotamers in protein crystal structures Bioinformatics 22 1397 1398 1:CAS:528:DC%2BD28XmtlOjsbc%3D 10.1093/bioinformatics/btl128 (Pubitemid 43985277)
-
(2006)
Bioinformatics
, vol.22
, Issue.11
, pp. 1397-1398
-
-
Weichenberger, C.X.1
Sippl, M.J.2
-
25
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
DOI 10.1021/ja981844+
-
J Srinivasan TE Cheatham P Cieplak PA Kollman DA Case 1998 Continuum solvent studies of the stability of DNA, RNA and phosphoramidate-DNA helices J Am Chem Soc 120 9401 9409 1:CAS:528:DyaK1cXlsVyqtLo%3D 10.1021/ja981844+ (Pubitemid 28452628)
-
(1998)
Journal of the American Chemical Society
, vol.120
, Issue.37
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham III, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
26
-
-
0042710087
-
Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
-
DOI 10.1021/ja990935j
-
I Massova PA Kollman 1999 Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies J Am Chem Soc 121 8133 8143 1:CAS:528:DyaK1MXlsFSktr0%3D 10.1021/ja990935j (Pubitemid 29444447)
-
(1999)
Journal of the American Chemical Society
, vol.121
, Issue.36
, pp. 8133-8143
-
-
Massova, I.1
Kollman, P.A.2
-
27
-
-
33846863158
-
Solvated Interaction Energy (SIE) for scoring protein-ligand binding affinities. 1. Exploring the parameter space
-
DOI 10.1021/ci600406v
-
M Naim S Bhat KN Rankin S Dennis SF Chowdhury I Siddiqi P Drabik T Sulea CI Bayly A Jakalian EO Purisima 2007 Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 1. exploring the parameter space J Chem Inf Model 47 122 133 10.1021/ci600406v (Pubitemid 46225568)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.1
, pp. 122-133
-
-
Naim, M.1
Bhat, S.2
Rankin, K.N.3
Dennis, S.4
Chowdhury, S.F.5
Siddiqi, I.6
Drabik, P.7
Sulea, T.8
Bayly, C.I.9
Jakalian, A.10
Purisima, E.O.11
-
28
-
-
58149327312
-
An improved method to predict the entropy term with the MM/PBSA approach
-
1:CAS:528:DC%2BD1MXmtFGn 10.1007/s10822-008-9238-z
-
J Kongsted U Ryde 2009 An improved method to predict the entropy term with the MM/PBSA approach J Comput Aided Mol Des 23 63 71 1:CAS:528: DC%2BD1MXmtFGn 10.1007/s10822-008-9238-z
-
(2009)
J Comput Aided Mol des
, vol.23
, pp. 63-71
-
-
Kongsted, J.1
Ryde, U.2
-
29
-
-
1842479952
-
Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
-
DOI 10.1002/prot.20033
-
A Onufriev D Bashford DA Case 2004 Exploring protein native states and large-scale conformational changes with a modified generalized born model Proteins 55 383 394 1:CAS:528:DC%2BD2cXjtFKhs78%3D 10.1002/prot.20033 (Pubitemid 38437495)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.2
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
30
-
-
0000658538
-
Langevin modes of macromolecules
-
1:CAS:528:DyaL2sXls1Sktw%3D%3D 10.1063/1.451373
-
G Lamm A Szabo 1986 Langevin modes of macromolecules J Chem Phys 85 7334 7348 1:CAS:528:DyaL2sXls1Sktw%3D%3D 10.1063/1.451373
-
(1986)
J Chem Phys
, vol.85
, pp. 7334-7348
-
-
Lamm, G.1
Szabo, A.2
-
31
-
-
0025292904
-
Langevin modes of macromolecules: Applications to crambin and DNA hexamers
-
DOI 10.1002/bip.360291008
-
J Kottalam DA Case 1990 Langevin modes of macromolecules-applications to Crambin and Dna hexamers Biopolymers 29 1409 1421 1:CAS:528:DyaK3cXkslCiu7w%3D 10.1002/bip.360291008 (Pubitemid 20180262)
-
(1990)
Biopolymers
, vol.29
, Issue.10-11
, pp. 1409-1421
-
-
Kottalam, J.1
Case, D.A.2
-
32
-
-
0028331255
-
Normal-mode analysis of protein dynamics
-
1:CAS:528:DyaK2cXltVehsbY%3D 10.1016/S0959-440X(94)90321-2
-
DA Case 1994 Normal-mode analysis of protein dynamics Curr Opin Struct Biol 4 285 290 1:CAS:528:DyaK2cXltVehsbY%3D 10.1016/S0959-440X(94)90321-2
-
(1994)
Curr Opin Struct Biol
, vol.4
, pp. 285-290
-
-
Case, D.A.1
-
33
-
-
13844312649
-
ZINC - A free database of commercially available compounds for virtual screening
-
DOI 10.1021/ci049714+
-
JJ Irwin BK Shoichet 2005 ZINC-a free database of commercially available compounds for virtual screening J Chem Inf Model 45 177 182 1:CAS:528: DC%2BD2cXhtVOjt77J 10.1021/ci049714+ (Pubitemid 40736970)
-
(2005)
Journal of Chemical Information and Modeling
, vol.45
, Issue.1
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
34
-
-
75549090213
-
KEGG for representation and analysis of molecular networks involving diseases and drugs
-
1:CAS:528:DC%2BC3cXktlygtg%3D%3D 10.1093/nar/gkp896
-
M Kanehisa S Goto M Furumichi M Tanabe M Hirakawa 2010 KEGG for representation and analysis of molecular networks involving diseases and drugs Nucleic Acids Res 38 D355 D360 1:CAS:528:DC%2BC3cXktlygtg%3D%3D 10.1093/nar/gkp896
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Kanehisa, M.1
Goto, S.2
Furumichi, M.3
Tanabe, M.4
Hirakawa, M.5
-
35
-
-
0032729435
-
Exploring expression data: Identification and analysis of coexpressed genes
-
1:CAS:528:DyaK1MXns12ktrc%3D 10.1101/gr.9.11.1106
-
LJ Heyer S Kruglyak S Yooseph 1999 Exploring expression data: identification and analysis of coexpressed genes Genome Res 9 1106 1115 1:CAS:528:DyaK1MXns12ktrc%3D 10.1101/gr.9.11.1106
-
(1999)
Genome Res
, vol.9
, pp. 1106-1115
-
-
Heyer, L.J.1
Kruglyak, S.2
Yooseph, S.3
-
36
-
-
33745359822
-
The blue obelisk - Interoperability in chemical informatics
-
DOI 10.1021/ci050400b
-
R Guha MT Howard GR Hutchison P Murray-Rust H Rzepa C Steinbeck J Wegner EL Willighagen 2006 The Blue Obelisk-interoperability in chemical informatics J Chem Inf Model 46 991 998 1:CAS:528:DC%2BD28Xhs1Wjsbw%3D 10.1021/ci050400b (Pubitemid 43999142)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.3
, pp. 991-998
-
-
Guha, R.1
Howard, M.T.2
Hutchison, G.R.3
Murray-Rust, P.4
Rzepa, H.5
Steinbeck, C.6
Wegner, J.7
Willighagen, E.L.8
|