-
1
-
-
84986522918
-
ICM: A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
-
doi:10.1002/jcc.540150503
-
Abagyan R, Totrov M, Kuznetsov D (1994) ICM: A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J Comput Chem 15: 488-506. doi: 10. 1002/jcc. 540150503.
-
(1994)
J Comput Chem
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
2
-
-
0002833057
-
Docking small ligands in flexible binding sites
-
doi:10.1002/(SICI)1096-987X(19980115)19:1<21::AID-JCC2>3.0.CO;2-0
-
Apostolakis J, Plückthun A, Caflisch A (1998) Docking small ligands in flexible binding sites. J Comput Chem 19: 21-37. doi: 10. 1002/(SICI)1096-987X(19980115)19: 1<21:: AID-JCC2>3. 0. CO;2-0.
-
(1998)
J Comput Chem
, vol.19
, pp. 21-37
-
-
Apostolakis, J.1
Plückthun, A.2
Caflisch, A.3
-
3
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Aqvist J, Medina C, Samuelsson JE (1994) A new method for predicting binding affinity in computer-aided drug design. Protein Eng 7: 385-391.
-
(1994)
Protein Eng
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
4
-
-
73949141783
-
An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics
-
doi:10.1021/ct900262t
-
Armen RS, Chen J, Brooks CL (2009) An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. J Chem Theory Comput 5: 2909-2923. doi: 10. 1021/ct900262t.
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 2909-2923
-
-
Armen, R.S.1
Chen, J.2
Brooks, C.L.3
-
5
-
-
84857782921
-
Exploring c-Met kinase flexibility by sampling and clustering its conformational space
-
doi:10.1002/prot.24021
-
Asses Y, Venkatraman V, Leroux V et al (2012) Exploring c-Met kinase flexibility by sampling and clustering its conformational space. Proteins Struct Funct Bioinform 80: 1227-1238. doi: 10. 1002/prot. 24021.
-
(2012)
Proteins Struct Funct Bioinform
, vol.80
, pp. 1227-1238
-
-
Asses, Y.1
Venkatraman, V.2
Leroux, V.3
-
6
-
-
77952825581
-
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking
-
doi:10.1093/bioinformatics/btq112
-
Ballester PJ, Mitchell JBO (2010) A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking. Bioinformatics 26: 1169-1175. doi: 10. 1093/bioinformatics/btq112.
-
(2010)
Bioinformatics
, vol.26
, pp. 1169-1175
-
-
Ballester, P.J.1
Mitchell, J.B.O.2
-
7
-
-
0032533791
-
Flexible docking using Tabu search and an empirical estimate of binding affinity
-
Baxter CA, Murray CW, Clark DE et al (1998) Flexible docking using Tabu search and an empirical estimate of binding affinity. Proteins 33: 367-382.
-
(1998)
Proteins
, vol.33
, pp. 367-382
-
-
Baxter, C.A.1
Murray, C.W.2
Clark, D.E.3
-
8
-
-
77950207644
-
Tackling the challenges posed by target flexibility in drug design
-
doi:10.1517/17460441003713462
-
Beier C, Zacharias M (2010) Tackling the challenges posed by target flexibility in drug design. Expert Opin Drug Discov 5: 347-359. doi: 10. 1517/17460441003713462.
-
(2010)
Expert Opin Drug Discov
, vol.5
, pp. 347-359
-
-
Beier, C.1
Zacharias, M.2
-
9
-
-
0034649618
-
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
-
Bissantz C, Folkers G, Rognan D (2000) Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem 43: 4759-4767.
-
(2000)
J Med Chem
, vol.43
, pp. 4759-4767
-
-
Bissantz, C.1
Folkers, G.2
Rognan, D.3
-
10
-
-
0026813925
-
The computer program LUDI: a new method for the de novo design of enzyme inhibitors
-
Böhm HJ (1992) The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des 6: 61-78.
-
(1992)
J Comput Aided Mol Des
, vol.6
, pp. 61-78
-
-
Böhm, H.J.1
-
11
-
-
54949108677
-
-
American Chemical Society, Washington, DC
-
Bolton EE, Wang Y, Thiessen PA, Bryant SH (2008) Chapter 12 in. Annual Reports in Computational Chemistry, vol 4. American Chemical Society, Washington, DC, pp 217-241.
-
(2008)
Chapter 12 in. Annual Reports in Computational Chemistry, vol 4
, pp. 217-241
-
-
Bolton, E.E.1
Wang, Y.2
Thiessen, P.A.3
Bryant, S.H.4
-
12
-
-
63149162777
-
Managing protein flexibility in docking and its applications
-
doi:10.1016/j.drudis.2009.01.003
-
B-Rao C, Subramanian J, Sharma SD (2009) Managing protein flexibility in docking and its applications. Drug Discov Today 14: 394-400. doi: 10. 1016/j. drudis. 2009. 01. 003.
-
(2009)
Drug Discov Today
, vol.14
, pp. 394-400
-
-
B-Rao, C.1
Subramanian, J.2
Sharma, S.D.3
-
13
-
-
77953326788
-
Chemical space sampling by different scoring functions and crystal structures
-
doi:10.1007/s10822-010-9356-2
-
Brooijmans N, Humblet C (2010) Chemical space sampling by different scoring functions and crystal structures. J Comput Aided Mol Des 24: 433-447. doi: 10. 1007/s10822-010-9356-2.
-
(2010)
J Comput Aided Mol Des
, vol.24
, pp. 433-447
-
-
Brooijmans, N.1
Humblet, C.2
-
14
-
-
0042353897
-
Molecular recognition and docking algorithms
-
doi:10.1146/annurev.biophys.32.110601.142532
-
Brooijmans N, Kuntz ID (2003) Molecular recognition and docking algorithms. Annu Rev Biophys Biomol Struct 32: 335-373. doi: 10. 1146/annurev. biophys. 32. 110601. 142532.
-
(2003)
Annu Rev Biophys Biomol Struct
, vol.32
, pp. 335-373
-
-
Brooijmans, N.1
Kuntz, I.D.2
-
15
-
-
0036019065
-
Protein flexibility is an important component of structure-based drug discovery
-
Carlson HA (2002) Protein flexibility is an important component of structure-based drug discovery. Curr Pharm Des 8: 1571-1578.
-
(2002)
Curr Pharm Des
, vol.8
, pp. 1571-1578
-
-
Carlson, H.A.1
-
16
-
-
54749115273
-
Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility
-
doi:10.2174/157340908785747474
-
Cavasotto C, Singh N (2008) Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility. Curr Comput Aided-Drug Des 4: 221-234. doi: 10. 2174/157340908785747474.
-
(2008)
Curr Comput Aided-Drug Des
, vol.4
, pp. 221-234
-
-
Cavasotto, C.1
Singh, N.2
-
17
-
-
77957820654
-
Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina
-
doi:10.1371/journal.pone.0011955
-
Chang MW, Ayeni C, Breuer S, Torbett BE (2010) Virtual screening for HIV protease inhibitors: a comparison of AutoDock 4 and Vina. PLoS ONE 5: e11955. doi: 10. 1371/journal. pone. 0011955.
-
(2010)
PLoS ONE
, vol.5
-
-
Chang, M.W.1
Ayeni, C.2
Breuer, S.3
Torbett, B.E.4
-
18
-
-
80053539881
-
Conformational selection or induced-fit? 50 years of debate resolved
-
F1000, doi:10.3410/B3-19
-
Changeux J-P, Edelstein S (2011) Conformational selection or induced-fit? 50 years of debate resolved. Biol Rep. doi: 10. 3410/B3-19. F1000.
-
(2011)
Biol Rep
-
-
Changeux, J.-P.1
Edelstein, S.2
-
19
-
-
0033576680
-
Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
-
doi:10.1021/jm990352k
-
Charifson PS, Corkery JJ, Murcko MA, Walters WP (1999) Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins. J Med Chem 42: 5100-5109. doi: 10. 1021/jm990352k.
-
(1999)
J Med Chem
, vol.42
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
20
-
-
66149103553
-
Comparative Assessment of Scoring Functions on a Diverse Test Set
-
doi:10.1021/ci9000053
-
Cheng T, Li X, Li Y et al (2009) Comparative Assessment of Scoring Functions on a Diverse Test Set. J Chem Inf Model 49: 1079-1093. doi: 10. 1021/ci9000053.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1079-1093
-
-
Cheng, T.1
Li, X.2
Li, Y.3
-
21
-
-
84862795414
-
Structure-based virtual screening for drug discovery: a problem-centric review
-
doi:10.1208/s12248-012-9322-0
-
Cheng T, Li Q, Zhou Z et al (2012) Structure-based virtual screening for drug discovery: a problem-centric review. AAPS J 14: 133-141. doi: 10. 1208/s12248-012-9322-0.
-
(2012)
AAPS J
, vol.14
, pp. 133-141
-
-
Cheng, T.1
Li, Q.2
Zhou, Z.3
-
22
-
-
0030203970
-
Evolutionary algorithms in computer-aided molecular design
-
doi:10.1007/BF00124503
-
Clark DE, Westhead DR (1996) Evolutionary algorithms in computer-aided molecular design. J Comput Aided Mol Des 10: 337-358. doi: 10. 1007/BF00124503.
-
(1996)
J Comput Aided Mol Des
, vol.10
, pp. 337-358
-
-
Clark, D.E.1
Westhead, D.R.2
-
24
-
-
77951992987
-
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
-
doi:10.1021/ci900407c
-
Craig IR, Essex JW, Spiegel K (2010) Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments. J Chem Inf Model 50: 511-524. doi: 10. 1021/ci900407c.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 511-524
-
-
Craig, I.R.1
Essex, J.W.2
Spiegel, K.3
-
25
-
-
84883209345
-
CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series
-
Damm-Ganamet KL, Smith RD, Dunbar JB et al (2013) CSAR Benchmark Exercise 2011-2012: Evaluation of Results from Docking and Relative Ranking of Blinded Congeneric Series. J. Chem. Inf. Model 53: 1853-1870.
-
(2013)
J. Chem. Inf. Model
, vol.53
, pp. 1853-1870
-
-
Damm-Ganamet, K.L.1
Smith, R.D.2
Dunbar, J.B.3
-
26
-
-
61449217240
-
Linear interaction energy (LIE) method in lead discovery and optimization
-
De Amorim HLN, Caceres RA, Netz PA (2008) Linear interaction energy (LIE) method in lead discovery and optimization. Curr Drug Targets 9: 1100-1105.
-
(2008)
Curr Drug Targets
, vol.9
, pp. 1100-1105
-
-
De Amorim, H.L.N.1
Caceres, R.A.2
Netz, P.A.3
-
27
-
-
61449172290
-
Computational methods for calculation of ligand-binding affinity
-
De Azevedo WF Jr, Dias R (2008) Computational methods for calculation of ligand-binding affinity. Curr Drug Targets 9: 1031-1039.
-
(2008)
Curr Drug Targets
, vol.9
, pp. 1031-1039
-
-
De Azevedo Jr., W.F.1
Dias, R.2
-
28
-
-
11344262474
-
Selection-Insertion Schemes in Genetic Algorithms for the Flexible Ligand Docking Problem
-
In: Deb K (ed), GECCO 2004. Springer, Berlin
-
de Magalhães CS, Barbosa HJC, Dardenne LE (2004a) Selection-Insertion Schemes in Genetic Algorithms for the Flexible Ligand Docking Problem. In: Deb K (ed) Genetic Evolutionary Computation, GECCO 2004. Springer, Berlin, pp 368-379.
-
(2004)
Genetic Evolutionary Computation
, pp. 368-379
-
-
de Magalhães, C.S.1
Barbosa, H.J.C.2
Dardenne, L.E.3
-
29
-
-
11344288637
-
A genetic algorithm for the ligand-protein docking problem
-
doi:10.1590/S1415-47572004000400022
-
de Magalhães CS, Barbosa HJC, Dardenne LE (2004b) A genetic algorithm for the ligand-protein docking problem. Genet Mol Biol 27: 605-610. doi: 10. 1590/S1415-47572004000400022.
-
(2004)
Genet Mol Biol
, vol.27
, pp. 605-610
-
-
de Magalhães, C.S.1
Barbosa, H.J.C.2
Dardenne, L.E.3
-
30
-
-
0031020376
-
Computation of the binding of fully flexible peptides to proteins with flexible side chains
-
Desmet J, Wilson IA, Joniau M et al (1997) Computation of the binding of fully flexible peptides to proteins with flexible side chains. FASEB J 11: 164-172.
-
(1997)
FASEB J
, vol.11
, pp. 164-172
-
-
Desmet, J.1
Wilson, I.A.2
Joniau, M.3
-
31
-
-
84859166785
-
On the applicability of elastic network normal modes in small-molecule docking
-
doi:10.1021/ci2004847
-
Dietzen M, Zotenko E, Hildebrandt A, Lengauer T (2012) On the applicability of elastic network normal modes in small-molecule docking. J Chem Inf Model 52: 844-856. doi: 10. 1021/ci2004847.
-
(2012)
J Chem Inf Model
, vol.52
, pp. 844-856
-
-
Dietzen, M.1
Zotenko, E.2
Hildebrandt, A.3
Lengauer, T.4
-
32
-
-
0037161605
-
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B
-
Doman TN, McGovern SL, Witherbee BJ et al (2002) Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 45: 2213-2221.
-
(2002)
J Med Chem
, vol.45
, pp. 2213-2221
-
-
Doman, T.N.1
McGovern, S.L.2
Witherbee, B.J.3
-
33
-
-
33644878571
-
SuperNatural: a searchable database of available natural compounds
-
doi:10.1093/nar/gkj132
-
Dunkel M (2006) SuperNatural: a searchable database of available natural compounds. Nucleic Acids Res 34: D678-D683. doi: 10. 1093/nar/gkj132.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Dunkel, M.1
-
34
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge MD, Murray CW, Auton TR et al (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 11: 425-445.
-
(1997)
J Comput Aided Mol Des
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
-
35
-
-
0035025191
-
DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases
-
Ewing TJ, Makino S, Skillman AG, Kuntz ID (2001) DOCK 4. 0: search strategies for automated molecular docking of flexible molecule databases. J Comput Aided Mol Des 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
-
36
-
-
33748667774
-
Consensus scoring for protein-ligand interactions
-
doi:10.1016/j.drudis.2006.03.009
-
Feher M (2006) Consensus scoring for protein-ligand interactions. Drug Discov Today 11: 421-428. doi: 10. 1016/j. drudis. 2006. 03. 009.
-
(2006)
Drug Discov Today
, vol.11
, pp. 421-428
-
-
Feher, M.1
-
37
-
-
4744365803
-
Soft docking and multiple receptor conformations in virtual screening
-
doi:10.1021/jm049756p
-
Ferrari AM, Wei BQ, Costantino L, Shoichet BK (2004) Soft docking and multiple receptor conformations in virtual screening. J Med Chem 47: 5076-5084. doi: 10. 1021/jm049756p.
-
(2004)
J Med Chem
, vol.47
, pp. 5076-5084
-
-
Ferrari, A.M.1
Wei, B.Q.2
Costantino, L.3
Shoichet, B.K.4
-
38
-
-
84867743951
-
Modeling loop backbone flexibility in receptor-ligand docking simulations
-
doi:10.1002/jcc.23087
-
Flick J, Tristram F, Wenzel W (2012) Modeling loop backbone flexibility in receptor-ligand docking simulations. J Comput Chem 33: 2504-2515. doi: 10. 1002/jcc. 23087.
-
(2012)
J Comput Chem
, vol.33
, pp. 2504-2515
-
-
Flick, J.1
Tristram, F.2
Wenzel, W.3
-
39
-
-
84863635369
-
The fundamental role of flexibility on the strength of molecular binding
-
doi:10.1039/c2sm25160d
-
Forrey C, Douglas JF, Gilson MK (2012) The fundamental role of flexibility on the strength of molecular binding. Soft Matter 8: 6385. doi: 10. 1039/c2sm25160d.
-
(2012)
Soft Matter
, vol.8
, pp. 6385
-
-
Forrey, C.1
Douglas, J.F.2
Gilson, M.K.3
-
40
-
-
12144289984
-
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
-
doi:10.1021/jm0306430
-
Friesner RA, Banks JL, Murphy RB et al (2004) Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. J Med Chem 47: 1739-1749. doi: 10. 1021/jm0306430.
-
(2004)
J Med Chem
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
-
41
-
-
33750124980
-
Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
doi:10.1021/jm051256o
-
Friesner RA, Murphy RB, Repasky MP et al (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 49: 6177-6196. doi: 10. 1021/jm051256o.
-
(2006)
J Med Chem
, vol.49
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
-
42
-
-
0037379786
-
Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities
-
doi:10.1016/S0006-3495(03)75033-4
-
Frimurer TM, Peters GH, Iversen LF et al (2003) Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities. Biophys J 84: 2273-2281. doi: 10. 1016/S0006-3495(03)75033-4.
-
(2003)
Biophys J
, vol.84
, pp. 2273-2281
-
-
Frimurer, T.M.1
Peters, G.H.2
Iversen, L.F.3
-
43
-
-
77956607370
-
Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein - Ligand Binding Affinities
-
doi:10.1021/ct1002913
-
Gallicchio E, Lapelosa M, Levy RM (2010) Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein - Ligand Binding Affinities. J Chem Theory Comput 6: 2961-2977. doi: 10. 1021/ct1002913.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 2961-2977
-
-
Gallicchio, E.1
Lapelosa, M.2
Levy, R.M.3
-
44
-
-
0000577041
-
Large-amplitude nonlinear motions in proteins
-
García (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68: 2696-2699.
-
(1992)
Phys Rev Lett
, vol.68
, pp. 2696-2699
-
-
García1
-
45
-
-
84862192766
-
ChEMBL: a large-scale bioactivity database for drug discovery
-
doi:10.1093/nar/gkr777
-
Gaulton A, Bellis LJ, Bento AP et al (2011) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40: D1100-D1107. doi: 10. 1093/nar/gkr777.
-
(2011)
Nucleic Acids Res
, vol.40
-
-
Gaulton, A.1
Bellis, L.J.2
Bento, A.P.3
-
46
-
-
0025135112
-
Automated docking of substrates to proteins by simulated annealing
-
doi:10.1002/prot.340080302
-
Goodsell DS, Olson AJ (1990) Automated docking of substrates to proteins by simulated annealing. Proteins 8: 195-202. doi: 10. 1002/prot. 340080302.
-
(1990)
Proteins
, vol.8
, pp. 195-202
-
-
Goodsell, D.S.1
Olson, A.J.2
-
47
-
-
84855925859
-
Linear interaction energy: method and applications in drug design
-
doi:10.1007/978-1-61779-465-0_20
-
Gutiérrez-de-Terán H, Aqvist J (2012) Linear interaction energy: method and applications in drug design. Methods Mol Biol (Clifton NJ) 819: 305-323. doi: 10. 1007/978-1-61779-465-0_20.
-
(2012)
Methods Mol Biol (Clifton NJ)
, vol.819
, pp. 305-323
-
-
Gutiérrez-De-Terán, H.1
Aqvist, J.2
-
48
-
-
79960244405
-
Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approachs
-
doi: 10. 1021/ci100469n
-
Haider MK, Bertrand H-O, Hubbard RE (2011) Predicting Fragment Binding Poses Using a Combined MCSS MM-GBSA Approach. J Chem Inf Model 51: 1092-1105. doi: 10. 1021/ci100469n.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 1092-1105
-
-
Haider, M.K.1
Bertrand, H.-O.2
Hubbard, R.E.3
-
49
-
-
0037571112
-
Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
-
doi:10.1002/(SICI)1096-987X(199604)17:5/6<490::AID-JCC1>3.0.CO;2-P
-
Halgren TA (1996) Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem 17: 490-519. doi: 10. 1002/(SICI)1096-987X(199604)17: 5/6<490:: AID-JCC1>3. 0. CO;2-P.
-
(1996)
J Comput Chem
, vol.17
, pp. 490-519
-
-
Halgren, T.A.1
-
50
-
-
81355147200
-
Investigation on the binding mode of benzothiophene analogues as potent factor IXa (FIXa) inhibitors in thrombosis by CoMFA, docking and molecular dynamic studies
-
doi:10.3109/14756366.2011.554414
-
Hao M, Li Y, Zhang S-W, Yang W (2011) Investigation on the binding mode of benzothiophene analogues as potent factor IXa (FIXa) inhibitors in thrombosis by CoMFA, docking and molecular dynamic studies. J Enzyme Inhib Med Chem 26: 792-804. doi: 10. 3109/14756366. 2011. 554414.
-
(2011)
J Enzyme Inhib Med Chem
, vol.26
, pp. 792-804
-
-
Hao, M.1
Li, Y.2
Zhang, S.-W.3
Yang, W.4
-
51
-
-
0031915558
-
Active-site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant
-
doi:10.1002/pro.5560070209
-
Hong L, Hartsuck JA, Foundling S et al (1998) Active-site mobility in human immunodeficiency virus, type 1, protease as demonstrated by crystal structure of A28S mutant. Protein Sci 7: 300-305. doi: 10. 1002/pro. 5560070209.
-
(1998)
Protein Sci
, vol.7
, pp. 300-305
-
-
Hong, L.1
Hartsuck, J.A.2
Foundling, S.3
-
52
-
-
84874445951
-
Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
-
doi:10.1021/ci300399w
-
Houston DR, Walkinshaw MD (2013) Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context. J Chem Inf Model 53: 384-390. doi: 10. 1021/ci300399w.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 384-390
-
-
Houston, D.R.1
Walkinshaw, M.D.2
-
53
-
-
77957899529
-
Advances and Challenges in Protein-Ligand Docking
-
doi:10.3390/ijms11083016
-
Huang S-Y, Zou X (2010) Advances and Challenges in Protein-Ligand Docking. Int J Mol Sci 11: 3016-3034. doi: 10. 3390/ijms11083016.
-
(2010)
Int J Mol Sci
, vol.11
, pp. 3016-3034
-
-
Huang, S.-Y.1
Zou, X.2
-
54
-
-
33750991346
-
Benchmarking Sets for Molecular Docking
-
doi:10.1021/jm0608356
-
Huang N, Shoichet BK, Irwin JJ (2006) Benchmarking Sets for Molecular Docking. J Med Chem 49: 6789-6801. doi: 10. 1021/jm0608356.
-
(2006)
J Med Chem
, vol.49
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
55
-
-
40549141789
-
Flexible protein-flexible ligand docking with disrupted velocity simulated annealing
-
doi:10.1002/prot.21781
-
Huang Z, Wong CF, Wheeler RA (2008) Flexible protein-flexible ligand docking with disrupted velocity simulated annealing. Proteins 71: 440-454. doi: 10. 1002/prot. 21781.
-
(2008)
Proteins
, vol.71
, pp. 440-454
-
-
Huang, Z.1
Wong, C.F.2
Wheeler, R.A.3
-
56
-
-
77957898063
-
Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions
-
doi:10.1039/c0cp00151a
-
Huang S-Y, Grinter SZ, Zou X (2010) Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys Chem Chem Phys 12: 12899-12908. doi: 10. 1039/c0cp00151a.
-
(2010)
Phys Chem Chem Phys
, vol.12
, pp. 12899-12908
-
-
Huang, S.-Y.1
Grinter, S.Z.2
Zou, X.3
-
57
-
-
84864199587
-
ZINC: A Free Tool to Discover Chemistry for Biology
-
doi:10.1021/ci3001277
-
Irwin JJ, Sterling T, Mysinger MM et al (2012) ZINC: A Free Tool to Discover Chemistry for Biology. J Chem Inf Model 52: 1757-1768. doi: 10. 1021/ci3001277.
-
(2012)
J Chem Inf Model
, vol.52
, pp. 1757-1768
-
-
Irwin, J.J.1
Sterling, T.2
Mysinger, M.M.3
-
58
-
-
0346996357
-
Improving Structure-Based Virtual Screening by Multivariate Analysis of Scoring Data
-
doi:10.1021/jm030896t
-
Jacobsson M, Lidén P, Stjernschantz E et al (2003) Improving Structure-Based Virtual Screening by Multivariate Analysis of Scoring Data. J Med Chem 46: 5781-5789. doi: 10. 1021/jm030896t.
-
(2003)
J Med Chem
, vol.46
, pp. 5781-5789
-
-
Jacobsson, M.1
Lidén, P.2
Stjernschantz, E.3
-
59
-
-
0033969620
-
Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition
-
Jain AN (2000) Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition. J Comput Aided Mol Des 14: 199-213.
-
(2000)
J Comput Aided Mol Des
, vol.14
, pp. 199-213
-
-
Jain, A.N.1
-
60
-
-
41349106542
-
Recommendations for evaluation of computational methods
-
doi:10.1007/s10822-008-9196-5
-
Jain AN, Nicholls A (2008) Recommendations for evaluation of computational methods. J Comput Aided Mol Des 22: 133-139. doi: 10. 1007/s10822-008-9196-5.
-
(2008)
J Comput Aided Mol Des
, vol.22
, pp. 133-139
-
-
Jain, A.N.1
Nicholls, A.2
-
61
-
-
0026310932
-
Soft docking": matching of molecular surface cubes
-
Jiang F, Kim SH (1991) "Soft docking": matching of molecular surface cubes. J Mol Biol 219: 79-102.
-
(1991)
J Mol Biol
, vol.219
, pp. 79-102
-
-
Jiang, F.1
Kim, S.H.2
-
62
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
-
Jones G, Willett P, Glen RC (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245: 43-53.
-
(1995)
J Mol Biol
, vol.245
, pp. 43-53
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
-
63
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
doi:10.1006/jmbi.1996.0897
-
Jones G, Willett P, Glen RC et al (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267: 727-748. doi: 10. 1006/jmbi. 1996. 0897.
-
(1997)
J Mol Biol
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
-
64
-
-
73349107775
-
The effect of ligand-based tautomer and protomer prediction on structure-based virtual screening
-
doi:10.1021/ci900364w
-
Kalliokoski T, Salo HS, Lahtela-Kakkonen M, Poso A (2009) The effect of ligand-based tautomer and protomer prediction on structure-based virtual screening. J Chem Inf Model 49: 2742-2748. doi: 10. 1021/ci900364w.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 2742-2748
-
-
Kalliokoski, T.1
Salo, H.S.2
Lahtela-Kakkonen, M.3
Poso, A.4
-
65
-
-
78149473070
-
Allostery and population shift in drug discovery
-
doi:10.1016/j.coph.2010.09.002
-
Kar G, Keskin O, Gursoy A, Nussinov R (2010) Allostery and population shift in drug discovery. Curr Opin Pharmacol 10: 715-722. doi: 10. 1016/j. coph. 2010. 09. 002.
-
(2010)
Curr Opin Pharmacol
, vol.10
, pp. 715-722
-
-
Kar, G.1
Keskin, O.2
Gursoy, A.3
Nussinov, R.4
-
66
-
-
0035915338
-
Fully flexible low-mode docking: application to induced fit in HIV integrase
-
Keserû GM, Kolossváry I (2001) Fully flexible low-mode docking: application to induced fit in HIV integrase. J Am Chem Soc 123: 12708-12709.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 12708-12709
-
-
Keserû, G.M.1
Kolossváry, I.2
-
67
-
-
42649138533
-
Assessment of programs for ligand binding affinity prediction
-
doi:10.1002/jcc.20893
-
Kim R, Skolnick J (2008) Assessment of programs for ligand binding affinity prediction. J Comput Chem 29: 1316-1331. doi: 10. 1002/jcc. 20893.
-
(2008)
J Comput Chem
, vol.29
, pp. 1316-1331
-
-
Kim, R.1
Skolnick, J.2
-
68
-
-
70350001745
-
LigMatch: a multiple structure-based ligand matching method for 3D virtual screening
-
doi:10.1021/ci900204y
-
Kinnings SL, Jackson RM (2009) LigMatch: a multiple structure-based ligand matching method for 3D virtual screening. J Chem Inf Model 49: 2056-2066. doi: 10. 1021/ci900204y.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 2056-2066
-
-
Kinnings, S.L.1
Jackson, R.M.2
-
69
-
-
0031581852
-
Molecular docking to ensembles of protein structures
-
doi:10.1006/jmbi.1996.0776
-
Knegtel RM, Kuntz ID, Oshiro CM (1997) Molecular docking to ensembles of protein structures. J Mol Biol 266: 424-440. doi: 10. 1006/jmbi. 1996. 0776.
-
(1997)
J Mol Biol
, vol.266
, pp. 424-440
-
-
Knegtel, R.M.1
Kuntz, I.D.2
Oshiro, C.M.3
-
70
-
-
80054807339
-
Receptor flexibility in small-molecule docking calculations
-
doi:10.1002/wcms.29
-
Kokh DB, Wade RC, Wenzel W (2011) Receptor flexibility in small-molecule docking calculations. Wiley Interdiscip Rev Comput Mol Sci 1: 298-314. doi: 10. 1002/wcms. 29.
-
(2011)
Wiley Interdiscip Rev Comput Mol Sci
, vol.1
, pp. 298-314
-
-
Kokh, D.B.1
Wade, R.C.2
Wenzel, W.3
-
71
-
-
73449145345
-
Docking screens: right for the right reasons?
-
Kolb P, Irwin JJ (2009) Docking screens: right for the right reasons? Curr Top Med Chem 9: 755-770.
-
(2009)
Curr Top Med Chem
, vol.9
, pp. 755-770
-
-
Kolb, P.1
Irwin, J.J.2
-
72
-
-
0034521981
-
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
-
Kollman PA, Massova I, Reyes C et al (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33: 889-897.
-
(2000)
Acc Chem Res
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
-
73
-
-
0000147236
-
Low-mode conformational search elucidated: Application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP
-
doi:10.1002/(SICI)1096-987X(19991130)20:15<1671::AID-JCC7>3.0.CO;2-Y
-
Kolossváry I, Guida WC (1999) Low-mode conformational search elucidated: Application to C39H80 and flexible docking of 9-deazaguanine inhibitors into PNP. J Comput Chem 20: 1671-1684. doi: 10. 1002/(SICI)1096-987X(19991130)20: 15<1671:: AID-JCC7>3. 0. CO;2-Y.
-
(1999)
J Comput Chem
, vol.20
, pp. 1671-1684
-
-
Kolossváry, I.1
Guida, W.C.2
-
74
-
-
0002709663
-
Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3
-
doi:10.1002/1096-987X(20010115)22:1<21::AID-JCC3>3.0.CO;2-I
-
Kolossváry I, Keserû GM (2001) Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3. J Comput Chem 22: 21-30. doi: 10. 1002/1096-987X(20010115)22: 1<21:: AID-JCC3>3. 0. CO;2-I.
-
(2001)
J Comput Chem
, vol.22
, pp. 21-30
-
-
Kolossváry, I.1
Keserû, G.M.2
-
75
-
-
33751358567
-
PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design
-
M. Dorigo, L. M. Gambardella, and M. Birattari (Eds.), Berlin: Springer
-
Korb O, Stützle T, Exner TE (2006) PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design. In: Dorigo M, Gambardella LM, Birattari M et al (eds) Ant Colony Optimisation Swarm Intelligence. Springer, Berlin, pp 247-258.
-
(2006)
Ant Colony Optimisation Swarm Intelligence
, pp. 247-258
-
-
Korb, O.1
Stützle, T.2
Exner, T.E.3
-
76
-
-
62449330667
-
Empirical Scoring Functions for Advanced Protein - Ligand Docking with PLANTS
-
doi:10.1021/ci800298z
-
Korb O, Stützle T, Exner TE (2009) Empirical Scoring Functions for Advanced Protein - Ligand Docking with PLANTS. J Chem Inf Model 49: 84-96. doi: 10. 1021/ci800298z.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 84-96
-
-
Korb, O.1
Stützle, T.2
Exner, T.E.3
-
77
-
-
82355182425
-
The Ensemble Performance Index: An Improved Measure for Assessing Ensemble Pose Prediction Performance
-
doi:10.1021/ci2002796
-
Korb O, McCabe P, Cole J (2011) The Ensemble Performance Index: An Improved Measure for Assessing Ensemble Pose Prediction Performance. J Chem Inf Model 51: 2915-2919. doi: 10. 1021/ci2002796.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 2915-2919
-
-
Korb, O.1
McCabe, P.2
Cole, J.3
-
78
-
-
84861499934
-
Potential and Limitations of Ensemble Docking
-
doi:10.1021/ci2005934
-
Korb O, Olsson TSG, Bowden SJ et al (2012) Potential and Limitations of Ensemble Docking. J Chem Inf Model 52: 1262-1274. doi: 10. 1021/ci2005934.
-
(2012)
J Chem Inf Model
, vol.52
, pp. 1262-1274
-
-
Korb, O.1
Olsson, T.S.G.2
Bowden, S.J.3
-
79
-
-
74849085203
-
Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors
-
doi:10.1002/cmdc.200900314
-
Krüger DM, Evers A (2010) Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. Chem Med Chem 5: 148-158. doi: 10. 1002/cmdc. 200900314.
-
(2010)
Chem Med Chem
, vol.5
, pp. 148-158
-
-
Krüger, D.M.1
Evers, A.2
-
80
-
-
0002192615
-
A combinatorial algorithm for calculating ligand binding
-
doi:10.1002/jcc.540050105
-
Kuhl FS, Crippen GM, Friesen DK (1984) A combinatorial algorithm for calculating ligand binding. J Comput Chem 5: 24-34. doi: 10. 1002/jcc. 540050105.
-
(1984)
J Comput Chem
, vol.5
, pp. 24-34
-
-
Kuhl, F.S.1
Crippen, G.M.2
Friesen, D.K.3
-
81
-
-
80052948931
-
Consensus virtual screening approaches to predict protein ligands
-
doi:10.1016/j.ejmech.2011.05.026
-
Kukol A (2011) Consensus virtual screening approaches to predict protein ligands. Eur J Med Chem 46: 4661-4664. doi: 10. 1016/j. ejmech. 2011. 05. 026.
-
(2011)
Eur J Med Chem
, vol.46
, pp. 4661-4664
-
-
Kukol, A.1
-
82
-
-
53349145331
-
FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects
-
doi:10.1186/1471-2105-9-396
-
Lagorce D, Sperandio O, Galons H et al (2008) FAF-Drugs2: Free ADME/tox filtering tool to assist drug discovery and chemical biology projects. BMC Bioinform 9: 396. doi: 10. 1186/1471-2105-9-396.
-
(2008)
BMC Bioinform
, vol.9
, pp. 396
-
-
Lagorce, D.1
Sperandio, O.2
Galons, H.3
-
83
-
-
66449110287
-
DOCK 6: combining techniques to model RNA-small molecule complexes
-
doi:10.1261/rna.1563609
-
Lang PT, Brozell SR, Mukherjee S et al (2009) DOCK 6: combining techniques to model RNA-small molecule complexes. RNA 15: 1219-1230. doi: 10. 1261/rna. 1563609.
-
(2009)
Rna
, vol.15
, pp. 1219-1230
-
-
Lang, P.T.1
Brozell, S.R.2
Mukherjee, S.3
-
84
-
-
0028158936
-
Ligand docking to proteins with discrete side-chain flexibility
-
Leach AR (1994) Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol 235: 345-356.
-
(1994)
J Mol Biol
, vol.235
, pp. 345-356
-
-
Leach, A.R.1
-
85
-
-
77957225016
-
Test MM-PB/SA on True Conformational Ensembles of Protein - Ligand Complexes
-
doi:10.1021/ci100036a
-
Li Y, Liu Z, Wang R (2010) Test MM-PB/SA on True Conformational Ensembles of Protein - Ligand Complexes. J Chem Inf Model 50: 1682-1692. doi: 10. 1021/ci100036a.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1682-1692
-
-
Li, Y.1
Liu, Z.2
Wang, R.3
-
86
-
-
79955401050
-
Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation
-
doi:10.1021/ci100490w
-
Li L, Khanna M, Jo I et al (2011a) Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation. J Chem Inf Model 51: 755-759. doi: 10. 1021/ci100490w.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 755-759
-
-
Li, L.1
Khanna, M.2
Jo, I.3
-
87
-
-
82355186353
-
Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures
-
doi:10.1021/ci200257b
-
Li Y, Kim DJ, Ma W et al (2011b) Discovery of Novel Checkpoint Kinase 1 Inhibitors by Virtual Screening Based on Multiple Crystal Structures. J Chem Inf Model 51: 2904-2914. doi: 10. 1021/ci200257b.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 2904-2914
-
-
Li, Y.1
Kim, D.J.2
Ma, W.3
-
88
-
-
84875428269
-
ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein-Ligand Interactions
-
doi:10.1021/ci300493w
-
Li G-B, Yang L-L, Wang W-J et al (2013) ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein-Ligand Interactions. J Chem Inf Model 53: 592-600. doi: 10. 1021/ci300493w.
-
(2013)
J Chem Inf Model
, vol.53
, pp. 592-600
-
-
Li, G.-B.1
Yang, L.-L.2
Wang, W.-J.3
-
89
-
-
79960218748
-
Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations
-
doi:10.1021/bi2004558
-
Lill MA (2011) Efficient Incorporation of Protein Flexibility and Dynamics into Molecular Docking Simulations. Biochemistry (Mosc) 50: 6157-6169. doi: 10. 1021/bi2004558.
-
(2011)
Biochemistry (Mosc)
, vol.50
, pp. 6157-6169
-
-
Lill, M.A.1
-
90
-
-
33846108633
-
BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities
-
doi:10.1093/nar/gkl999
-
Liu T, Lin Y, Wen X et al (2007) BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities. Nucleic Acids Res 35: D198-D201. doi: 10. 1093/nar/gkl999.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Liu, T.1
Lin, Y.2
Wen, X.3
-
91
-
-
0035848409
-
Customized versus universal scoring functions: application to class I MHC-peptide binding free energy predictions
-
Logean A, Sette A, Rognan D (2001) Customized versus universal scoring functions: application to class I MHC-peptide binding free energy predictions. Bioorg Med Chem Lett 11: 675-679.
-
(2001)
Bioorg Med Chem Lett
, vol.11
, pp. 675-679
-
-
Logean, A.1
Sette, A.2
Rognan, D.3
-
92
-
-
84868643706
-
Protein-specific Scoring Method for Ligand Discovery
-
doi:10.1089/cmb.2012.0188
-
Lu I-L, Wang H (2012) Protein-specific Scoring Method for Ligand Discovery. J Comput Biol 19: 1215-1226. doi: 10. 1089/cmb. 2012. 0188.
-
(2012)
J Comput Biol
, vol.19
, pp. 1215-1226
-
-
Lu, I.-L.1
Wang, H.2
-
93
-
-
84986511247
-
A molecular mechanics/grid method for evaluation of ligand-receptor interactions
-
doi:10.1002/jcc.540160409
-
Luty BA, Wasserman ZR, Stouten PFW et al (1995) A molecular mechanics/grid method for evaluation of ligand-receptor interactions. J Comput Chem 16: 454-464. doi: 10. 1002/jcc. 540160409.
-
(1995)
J Comput Chem
, vol.16
, pp. 454-464
-
-
Luty, B.A.1
Wasserman, Z.R.2
Stouten, P.F.W.3
-
95
-
-
84880529288
-
Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments
-
doi:10.1007/s10822-013-9644-8
-
Madhavi Sastry G, Adzhigirey M, Day T et al (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 27: 221-234. doi: 10. 1007/s10822-013-9644-8.
-
(2013)
J Comput Aided Mol Des
, vol.27
, pp. 221-234
-
-
Madhavi Sastry, G.1
Adzhigirey, M.2
Day, T.3
-
96
-
-
80052286822
-
Homology modeling, docking, molecular dynamics simulation, and structural analyses of coxsakievirus B3 2A protease: an enzyme involved in the pathogenesis of inflammatory myocarditis
-
doi:10.1016/j.ijbiomac.2011.05.023
-
Maghsoudi AH, Khodagholi F, Hadi-Alijanvand H et al (2011) Homology modeling, docking, molecular dynamics simulation, and structural analyses of coxsakievirus B3 2A protease: an enzyme involved in the pathogenesis of inflammatory myocarditis. Int J Biol Macromol 49: 487-492. doi: 10. 1016/j. ijbiomac. 2011. 05. 023.
-
(2011)
Int J Biol Macromol
, vol.49
, pp. 487-492
-
-
Maghsoudi, A.H.1
Khodagholi, F.2
Hadi-Alijanvand, H.3
-
97
-
-
0033135477
-
Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
-
Mangoni M, Roccatano D, Di Nola A (1999) Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. Proteins 35: 153-162.
-
(1999)
Proteins
, vol.35
, pp. 153-162
-
-
Mangoni, M.1
Roccatano, D.2
Di Nola, A.3
-
98
-
-
84867746731
-
Probing the diverse landscape of protein flexibility and binding
-
doi:10.1016/j.sbi.2012.08.008
-
Marsh JA, Teichmann SA, Forman-Kay JD (2012) Probing the diverse landscape of protein flexibility and binding. Curr Opin Struct Biol 22: 643-650. doi: 10. 1016/j. sbi. 2012. 08. 008.
-
(2012)
Curr Opin Struct Biol
, vol.22
, pp. 643-650
-
-
Marsh, J.A.1
Teichmann, S.A.2
Forman-Kay, J.D.3
-
99
-
-
76249106208
-
Let's not forget tautomers
-
doi:10.1007/s10822-009-9303-2
-
Martin YC (2009) Let's not forget tautomers. J Comput Aided Mol Des 23: 693-704. doi: 10. 1007/s10822-009-9303-2.
-
(2009)
J Comput Aided Mol Des
, vol.23
, pp. 693-704
-
-
Martin, Y.C.1
-
100
-
-
33750056673
-
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility
-
doi:10.1002/prot.21086
-
Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65: 538-548. doi: 10. 1002/prot. 21086.
-
(2006)
Proteins
, vol.65
, pp. 538-548
-
-
Meiler, J.1
Baker, D.2
-
101
-
-
0030867610
-
Ligand binding to proteins: The binding landscape model
-
doi:10.1002/pro.5560061011
-
Miller DW, Dill KA (1997) Ligand binding to proteins: The binding landscape model. Protein Sci 6: 2166-2179. doi: 10. 1002/pro. 5560061011.
-
(1997)
Protein Sci
, vol.6
, pp. 2166-2179
-
-
Miller, D.W.1
Dill, K.A.2
-
102
-
-
0028412035
-
FLOG: a system to select "quasi-flexible" ligands complementary to a receptor of known three-dimensional structure
-
Miller MD, Kearsley SK, Underwood DJ, Sheridan RP (1994) FLOG: a system to select "quasi-flexible" ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 8: 153-174.
-
(1994)
J Comput Aided Mol Des
, vol.8
, pp. 153-174
-
-
Miller, M.D.1
Kearsley, S.K.2
Underwood, D.J.3
Sheridan, R.P.4
-
103
-
-
33646765220
-
Effective handling of induced-fit motion in flexible docking
-
doi:10.1002/prot.20931
-
Mizutani MY, Takamatsu Y, Ichinose T et al (2006) Effective handling of induced-fit motion in flexible docking. Proteins 63: 878-891. doi: 10. 1002/prot. 20931.
-
(2006)
Proteins
, vol.63
, pp. 878-891
-
-
Mizutani, M.Y.1
Takamatsu, Y.2
Ichinose, T.3
-
104
-
-
64049102289
-
Binding of Small-Molecule Ligands to Proteins: "What You See" Is Not Always "What You Get
-
Mobley DL, Dill KA (2009) Binding of Small-Molecule Ligands to Proteins: "What You See" Is Not Always "What You Get. Structure 17: 489-498.
-
(2009)
Structure
, vol.17
, pp. 489-498
-
-
Mobley, D.L.1
Dill, K.A.2
-
105
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go: Docking/scoring methods-a review
-
doi:10.1038/sj.bjp.0707515
-
Moitessier N, Englebienne P, Lee D et al (2009) Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go: Docking/scoring methods-a review. Br J Pharmacol 153: S7-S26. doi: 10. 1038/sj. bjp. 0707515.
-
(2009)
Br J Pharmacol
, vol.153
-
-
Moitessier, N.1
Englebienne, P.2
Lee, D.3
-
106
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
doi:10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B
-
Morris GM, Goodsell DS, Halliday RS et al (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19: 1639-1662. doi: 10. 1002/(SICI)1096-987X(19981115)19: 14<1639:: AID-JCC10>3. 0. CO;2-B.
-
(1998)
J Comput Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
-
107
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-
doi:10.1002/jcc.21256
-
Morris GM, Huey R, Lindstrom W et al (2009) AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem 30: 2785-2791. doi: 10. 1002/jcc. 21256.
-
(2009)
J Comput Chem
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
-
108
-
-
33749242403
-
PMF scoring revisited
-
doi:10.1021/jm050038s
-
Muegge I (2006) PMF scoring revisited. J Med Chem 49: 5895-5902. doi: 10. 1021/jm050038s.
-
(2006)
J Med Chem
, vol.49
, pp. 5895-5902
-
-
Muegge, I.1
-
109
-
-
37349085453
-
A Flexible Approach to Induced Fit Docking
-
doi:10.1021/jm070593p
-
Nabuurs SB, Wagener M, de Vlieg J (2007) A Flexible Approach to Induced Fit Docking. J Med Chem 50: 6507-6518. doi: 10. 1021/jm070593p.
-
(2007)
J Med Chem
, vol.50
, pp. 6507-6518
-
-
Nabuurs, S.B.1
Wagener, M.2
de Vlieg, J.3
-
110
-
-
84865265287
-
Docking and scoring with ICM: the benchmarking results and strategies for improvement
-
doi:10.1007/s10822-012-9547-0
-
Neves MAC, Totrov M, Abagyan R (2012) Docking and scoring with ICM: the benchmarking results and strategies for improvement. J Comput Aided Mol Des 26: 675-686. doi: 10. 1007/s10822-012-9547-0.
-
(2012)
J Comput Aided Mol Des
, vol.26
, pp. 675-686
-
-
Neves, M.A.C.1
Totrov, M.2
Abagyan, R.3
-
111
-
-
79959758718
-
Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening
-
doi:10.1021/ci200117n
-
Nichols SE, Baron R, Ivetac A, McCammon JA (2011) Predictive Power of Molecular Dynamics Receptor Structures in Virtual Screening. J Chem Inf Model 51: 1439-1446. doi: 10. 1021/ci200117n.
-
(2011)
J Chem Inf Model
, vol.51
, pp. 1439-1446
-
-
Nichols, S.E.1
Baron, R.2
Ivetac, A.3
McCammon, J.A.4
-
112
-
-
0025988461
-
Automatic creation of drug candidate structures based on receptor structure. Starting point for artificial lead generation
-
doi:10.1016/S0040-4020(01)86503-0
-
Nishibata Y, Itai A (1991) Automatic creation of drug candidate structures based on receptor structure. Starting point for artificial lead generation. Tetrahedron 47: 8985-8990. doi: 10. 1016/S0040-4020(01)86503-0.
-
(1991)
Tetrahedron
, vol.47
, pp. 8985-8990
-
-
Nishibata, Y.1
Itai, A.2
-
113
-
-
0027517544
-
Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation
-
Nishibata Y, Itai A (1993) Confirmation of usefulness of a structure construction program based on three-dimensional receptor structure for rational lead generation. J Med Chem 36: 2921-2928.
-
(1993)
J Med Chem
, vol.36
, pp. 2921-2928
-
-
Nishibata, Y.1
Itai, A.2
-
115
-
-
84874646837
-
The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics†
-
doi:10.1002/jcc.23192
-
Nowosielski M, Hoffmann M, Kuron A et al (2013) The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics†. J Comput Chem 34: 750-756. doi: 10. 1002/jcc. 23192.
-
(2013)
J Comput Chem
, vol.34
, pp. 750-756
-
-
Nowosielski, M.1
Hoffmann, M.2
Kuron, A.3
-
116
-
-
33244478322
-
Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein - Ligand Complexes
-
doi:10.1021/ci050283k
-
Oda A, Tsuchida K, Takakura T et al (2006) Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein - Ligand Complexes. J Chem Inf Model 46: 380-391. doi: 10. 1021/ci050283k.
-
(2006)
J Chem Inf Model
, vol.46
, pp. 380-391
-
-
Oda, A.1
Tsuchida, K.2
Takakura, T.3
-
117
-
-
77953325281
-
Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles
-
doi:10.1007/s10822-010-9362-4
-
Park S-J, Kufareva I, Abagyan R (2010) Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles. J Comput Aided Mol Des 24: 459-471. doi: 10. 1007/s10822-010-9362-4.
-
(2010)
J Comput Aided Mol Des
, vol.24
, pp. 459-471
-
-
Park, S.-J.1
Kufareva, I.2
Abagyan, R.3
-
118
-
-
0027212356
-
Substrate mobility in thiocamphor-bound cytochrome P450cam: an explanation of the conflict between the observed product profile and the X-ray structure
-
Paulsen MD, Ornstein RL (1993) Substrate mobility in thiocamphor-bound cytochrome P450cam: an explanation of the conflict between the observed product profile and the X-ray structure. Protein Eng 6: 359-365.
-
(1993)
Protein Eng
, vol.6
, pp. 359-365
-
-
Paulsen, M.D.1
Ornstein, R.L.2
-
119
-
-
68149156015
-
E-novo: an automated workflow for efficient structure-based lead optimization
-
doi:10.1021/ci900073k
-
Pearce BC, Langley DR, Kang J et al (2009) E-novo: an automated workflow for efficient structure-based lead optimization. J Chem Inf Model 49: 1797-1809. doi: 10. 1021/ci900073k.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1797-1809
-
-
Pearce, B.C.1
Langley, D.R.2
Kang, J.3
-
120
-
-
33644843080
-
PSI-DOCK: towards highly efficient and accurate flexible ligand docking
-
doi:10.1002/prot.20790
-
Pei J, Wang Q, Liu Z et al (2006) PSI-DOCK: towards highly efficient and accurate flexible ligand docking. Proteins 62: 934-946. doi: 10. 1002/prot. 20790.
-
(2006)
Proteins
, vol.62
, pp. 934-946
-
-
Pei, J.1
Wang, Q.2
Liu, Z.3
-
121
-
-
84878652881
-
The role of protonation states in ligand-receptor recognition and binding
-
Petukh M, Stefl S, Alexov E (2013) The role of protonation states in ligand-receptor recognition and binding. Curr Pharm Des 19: 4182-4190.
-
(2013)
Curr Pharm Des
, vol.19
, pp. 4182-4190
-
-
Petukh, M.1
Stefl, S.2
Alexov, E.3
-
122
-
-
0036893503
-
Kinase inhibitors and the case for CH.O hydrogen bonds in protein-ligand binding
-
doi:10.1002/prot.10259
-
Pierce AC, Sandretto KL, Bemis GW (2002) Kinase inhibitors and the case for CH.O hydrogen bonds in protein-ligand binding. Proteins 49: 567-576. doi: 10. 1002/prot. 10259.
-
(2002)
Proteins
, vol.49
, pp. 567-576
-
-
Pierce, A.C.1
Sandretto, K.L.2
Bemis, G.W.3
-
123
-
-
79251524915
-
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
-
doi:10.1002/jcc.21643
-
Plewczynski D, Łaźniewski M, Augustyniak R, Ginalski K (2011) Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J Comput Chem 32: 742-755. doi: 10. 1002/jcc. 21643.
-
(2011)
J Comput Chem
, vol.32
, pp. 742-755
-
-
Plewczynski, D.1
Łaźniewski, M.2
Augustyniak, R.3
Ginalski, K.4
-
124
-
-
0029197510
-
Time-efficient docking of flexible ligands into active sites of proteins
-
Rarey M, Kramer B, Lengauer T (1995) Time-efficient docking of flexible ligands into active sites of proteins. Proc Int Conf Intell Syst Mol Biol 3: 300-308.
-
(1995)
Proc Int Conf Intell Syst Mol Biol
, vol.3
, pp. 300-308
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
125
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
doi:10.1006/jmbi.1996.0477
-
Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261: 470-489. doi: 10. 1006/jmbi. 1996. 0477.
-
(1996)
J Mol Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
126
-
-
0031181870
-
Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention
-
Rarey M, Kramer B, Lengauer T (1997) Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention. J Comput Aided Mol Des 11: 369-384.
-
(1997)
J Comput Aided Mol Des
, vol.11
, pp. 369-384
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
127
-
-
0029829066
-
Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors
-
Rejto PA, Verkhivker GM (1996) Unraveling principles of lead discovery: from unfrustrated energy landscapes to novel molecular anchors. Proc Natl Acad Sci USA 93: 8945-8950.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 8945-8950
-
-
Rejto, P.A.1
Verkhivker, G.M.2
-
128
-
-
79956024935
-
State-of-the-art in ligand-based virtual screening
-
doi:10.1016/j.drudis.2011.02.011
-
Ripphausen P, Nisius B, Bajorath J (2011) State-of-the-art in ligand-based virtual screening. Drug Discov Today 16: 372-376. doi: 10. 1016/j. drudis. 2011. 02. 011.
-
(2011)
Drug Discov Today
, vol.16
, pp. 372-376
-
-
Ripphausen, P.1
Nisius, B.2
Bajorath, J.3
-
129
-
-
65249120827
-
Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes
-
doi:10.1021/ci8003732
-
Rueda M, Bottegoni G, Abagyan R (2009) Consistent Improvement of Cross-Docking Results Using Binding Site Ensembles Generated with Elastic Network Normal Modes. J Chem Inf Model 49: 716-725. doi: 10. 1021/ci8003732.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 716-725
-
-
Rueda, M.1
Bottegoni, G.2
Abagyan, R.3
-
130
-
-
75749093371
-
Recipes for the Selection of Experimental Protein Conformations for Virtual Screening
-
doi:10.1021/ci9003943
-
Rueda M, Bottegoni G, Abagyan R (2010) Recipes for the Selection of Experimental Protein Conformations for Virtual Screening. J Chem Inf Model 50: 186-193. doi: 10. 1021/ci9003943.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 186-193
-
-
Rueda, M.1
Bottegoni, G.2
Abagyan, R.3
-
131
-
-
0031717170
-
Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization
-
Schaffer L, Verkhivker GM (1998) Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins 33: 295-310.
-
(1998)
Proteins
, vol.33
, pp. 295-310
-
-
Schaffer, L.1
Verkhivker, G.M.2
-
132
-
-
66149105428
-
Beyond the virtual screening paradigm: structure-based searching for new lead compounds
-
doi:10.1021/ci9000212
-
Schlosser J, Rarey M (2009) Beyond the virtual screening paradigm: structure-based searching for new lead compounds. J Chem Inf Model 49: 800-809. doi: 10. 1021/ci9000212.
-
(2009)
J Chem Inf Model
, vol.49
, pp. 800-809
-
-
Schlosser, J.1
Rarey, M.2
-
133
-
-
0033674405
-
Virtual screening with solvation and ligand-induced complementarity
-
doi:10.1023/A:1008737207775
-
Schnecke V, Kuhn L (2000) Virtual screening with solvation and ligand-induced complementarity. Perspect Drug Discov Des 20: 171-190. doi: 10. 1023/A: 1008737207775.
-
(2000)
Perspect Drug Discov Des
, vol.20
, pp. 171-190
-
-
Schnecke, V.1
Kuhn, L.2
-
134
-
-
67349104587
-
Targeted scoring functions for virtual screening
-
doi:10.1016/j.drudis.2009.03.013
-
Seifert MHJ (2009) Targeted scoring functions for virtual screening. Drug Discov Today 14: 562-569. doi: 10. 1016/j. drudis. 2009. 03. 013.
-
(2009)
Drug Discov Today
, vol.14
, pp. 562-569
-
-
Seifert, M.H.J.1
-
135
-
-
31544450787
-
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects
-
doi:10.1021/jm050540c
-
Sherman W, Day T, Jacobson MP et al (2006) Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects. J Med Chem 49: 534-553. doi: 10. 1021/jm050540c.
-
(2006)
J Med Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
-
136
-
-
84871604119
-
GalaxyDock: Protein-Ligand Docking with Flexible Protein Side-chains
-
doi:10.1021/ci300342z
-
Shin W-H, Seok C (2012) GalaxyDock: Protein-Ligand Docking with Flexible Protein Side-chains. J Chem Inf Model 52: 3225-3232. doi: 10. 1021/ci300342z.
-
(2012)
J Chem Inf Model
, vol.52
, pp. 3225-3232
-
-
Shin, W.-H.1
Seok, C.2
-
138
-
-
0026209073
-
Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads
-
doi:10.1021/ci00003a004
-
Smellie AS, Crippen GM, Richards WG (1991) Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads. J Chem Inf Model 31: 386-392. doi: 10. 1021/ci00003a004.
-
(1991)
J Chem Inf Model
, vol.31
, pp. 386-392
-
-
Smellie, A.S.1
Crippen, G.M.2
Richards, W.G.3
-
139
-
-
77954027036
-
Estimates of ligand-binding affinities supported by quantum mechanical methods
-
doi:10.1007/s12539-010-0083-0
-
Söderhjelm P, Kongsted J, Genheden S, Ryde U (2010) Estimates of ligand-binding affinities supported by quantum mechanical methods. Interdiscip Sci Comput Life Sci 2: 21-37. doi: 10. 1007/s12539-010-0083-0.
-
(2010)
Interdiscip Sci Comput Life Sci
, vol.2
, pp. 21-37
-
-
Söderhjelm, P.1
Kongsted, J.2
Genheden, S.3
Ryde, U.4
-
140
-
-
84861232290
-
Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies
-
doi:10.1007/s00894-011-1150-0
-
Sokkar P, Sathis V, Ramachandran M (2011) Computational modeling on the recognition of the HRE motif by HIF-1: molecular docking and molecular dynamics studies. J Mol Model 18: 1691-1700. doi: 10. 1007/s00894-011-1150-0.
-
(2011)
J Mol Model
, vol.18
, pp. 1691-1700
-
-
Sokkar, P.1
Sathis, V.2
Ramachandran, M.3
-
141
-
-
18244402654
-
In situ cross-docking" to simultaneously address multiple targets
-
doi:10.1021/jm050075j
-
Sotriffer CA, Dramburg I (2005) "In situ cross-docking" to simultaneously address multiple targets. J Med Chem 48: 3122-3125. doi: 10. 1021/jm050075j.
-
(2005)
J Med Chem
, vol.48
, pp. 3122-3125
-
-
Sotriffer, C.A.1
Dramburg, I.2
-
142
-
-
77955627131
-
How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis
-
doi:10.1007/s00249-010-0592-0
-
Sperandio O, Mouawad L, Pinto E et al (2010) How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur Biophys J EBJ 39: 1365-1372. doi: 10. 1007/s00249-010-0592-0.
-
(2010)
Eur Biophys J EBJ
, vol.39
, pp. 1365-1372
-
-
Sperandio, O.1
Mouawad, L.2
Pinto, E.3
-
143
-
-
77952985827
-
Improved ligand-protein binding affinity predictions using multiple binding modes
-
doi:10.1016/j.bpj.2010.02.034
-
Stjernschantz E, Oostenbrink C (2010) Improved ligand-protein binding affinity predictions using multiple binding modes. Biophys J 98: 2682-2691. doi: 10. 1016/j. bpj. 2010. 02. 034.
-
(2010)
Biophys J
, vol.98
, pp. 2682-2691
-
-
Stjernschantz, E.1
Oostenbrink, C.2
-
144
-
-
0036280264
-
X-ray crystallographic structure of ABT-378 (lopinavir) bound to HIV-1 protease
-
Stoll V, Qin W, Stewart KD et al (2002) X-ray crystallographic structure of ABT-378 (lopinavir) bound to HIV-1 protease. Bioorg Med Chem 10: 2803-2806.
-
(2002)
Bioorg Med Chem
, vol.10
, pp. 2803-2806
-
-
Stoll, V.1
Qin, W.2
Stewart, K.D.3
-
145
-
-
80054983548
-
A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors
-
doi:10.1016/j.bmc.2011.09.023
-
Takaya D, Yamashita A, Kamijo K et al (2011) A new method for induced fit docking (GENIUS) and its application to virtual screening of novel HCV NS3-4A protease inhibitors. Bioorg Med Chem 19: 6892-6905. doi: 10. 1016/j. bmc. 2011. 09. 023.
-
(2011)
Bioorg Med Chem
, vol.19
, pp. 6892-6905
-
-
Takaya, D.1
Yamashita, A.2
Kamijo, K.3
-
146
-
-
0041989635
-
Conformational flexibility models for the receptor in structure based drug design
-
Teodoro ML, Kavraki LE (2003) Conformational flexibility models for the receptor in structure based drug design. Curr Pharm Des 9: 1635-1648.
-
(2003)
Curr Pharm Des
, vol.9
, pp. 1635-1648
-
-
Teodoro, M.L.1
Kavraki, L.E.2
-
147
-
-
0042894239
-
Understanding protein flexibility through dimensionality reduction
-
doi:10.1089/10665270360688228
-
Teodoro ML, Phillips GN Jr, Kavraki LE (2003) Understanding protein flexibility through dimensionality reduction. J Comput Biol 10: 617-634. doi: 10. 1089/10665270360688228.
-
(2003)
J Comput Biol
, vol.10
, pp. 617-634
-
-
Teodoro, M.L.1
Phillips Jr., G.N.2
Kavraki, L.E.3
-
148
-
-
78649501368
-
Prediction of protein-ligand binding affinities using multiple instance learning
-
doi:10.1016/j.jmgm.2010.09.006
-
Teramoto R, Kashima H (2010) Prediction of protein-ligand binding affinities using multiple instance learning. J Mol Graph Model 29: 492-497. doi: 10. 1016/j. jmgm. 2010. 09. 006.
-
(2010)
J Mol Graph Model
, vol.29
, pp. 492-497
-
-
Teramoto, R.1
Kashima, H.2
-
149
-
-
0035811458
-
A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities
-
Terp GE, Johansen BN, Christensen IT, Jørgensen FS (2001) A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities. J Med Chem 44: 2333-2343.
-
(2001)
J Med Chem
, vol.44
, pp. 2333-2343
-
-
Terp, G.E.1
Johansen, B.N.2
Christensen, I.T.3
Jørgensen, F.S.4
-
150
-
-
0345483185
-
Prodock: Software package for protein modeling and docking
-
doi:10.1002/(SICI)1096-987X(199903)20:4<412::AID-JCC3>3.0.CO;2-N
-
Trosset J-Y, Scheraga HA (1999) Prodock: Software package for protein modeling and docking. J Comput Chem 20: 412-427. doi: 10. 1002/(SICI)1096-987X(199903)20: 4<412:: AID-JCC3>3. 0. CO;2-N.
-
(1999)
J Comput Chem
, vol.20
, pp. 412-427
-
-
Trosset, J.-Y.1
Scheraga, H.A.2
-
151
-
-
0033621104
-
Folding and binding cascades: shifts in energy landscapes
-
Tsai CJ, Ma B, Nussinov R (1999) Folding and binding cascades: shifts in energy landscapes. Proc Natl Acad Sci USA 96: 9970-9972.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 9970-9972
-
-
Tsai, C.J.1
Ma, B.2
Nussinov, R.3
-
152
-
-
84855460321
-
Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches
-
doi:10.1098/rsif.2011.0584
-
Tuffery P, Derreumaux P (2011) Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches. J R Soc Interface 9: 20-33. doi: 10. 1098/rsif. 2011. 0584.
-
(2011)
J R Soc Interface
, vol.9
, pp. 20-33
-
-
Tuffery, P.1
Derreumaux, P.2
-
153
-
-
26444588137
-
DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
-
doi:10.1021/jm050436v
-
Velec HFG, Gohlke H, Klebe G (2005) DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem 48: 6296-6303. doi: 10. 1021/jm050436v.
-
(2005)
J Med Chem
, vol.48
, pp. 6296-6303
-
-
Velec, H.F.G.1
Gohlke, H.2
Klebe, G.3
-
154
-
-
84864418223
-
Flexible protein docking refinement using pose-dependent normal mode analysis
-
doi:10.1002/prot.24115
-
Venkatraman V, Ritchie DW (2012) Flexible protein docking refinement using pose-dependent normal mode analysis. Proteins 80: 2262-2274. doi: 10. 1002/prot. 24115.
-
(2012)
Proteins
, vol.80
, pp. 2262-2274
-
-
Venkatraman, V.1
Ritchie, D.W.2
-
156
-
-
2942721004
-
Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment
-
doi:10.1021/ci034289q
-
Verdonk ML, Berdini V, Hartshorn MJ et al (2004) Virtual Screening Using Protein-Ligand Docking: Avoiding Artificial Enrichment. J Chem Inf Model 44: 793-806. doi: 10. 1021/ci034289q.
-
(2004)
J Chem Inf Model
, vol.44
, pp. 793-806
-
-
Verdonk, M.L.1
Berdini, V.2
Hartshorn, M.J.3
-
157
-
-
0346731233
-
Multiple active site corrections for docking and virtual screening
-
doi:10.1021/jm030161o
-
Vigers GPA, Rizzi JP (2004) Multiple active site corrections for docking and virtual screening. J Med Chem 47: 80-89. doi: 10. 1021/jm030161o.
-
(2004)
J Med Chem
, vol.47
, pp. 80-89
-
-
Vigers, G.P.A.1
Rizzi, J.P.2
-
158
-
-
0029798563
-
Docking enzyme-inhibitor complexes using a preference-based free-energy surface
-
doi:10.1002/prot.1
-
Wallqvist A, Covell DG (1996) Docking enzyme-inhibitor complexes using a preference-based free-energy surface. Proteins 25: 403-419. doi: 10. 1002/prot. 1.
-
(1996)
Proteins
, vol.25
, pp. 403-419
-
-
Wallqvist, A.1
Covell, D.G.2
-
159
-
-
84877823202
-
Scoring functions for prediction of protein-ligand interactions
-
Wang J-C, Lin J-H (2013) Scoring functions for prediction of protein-ligand interactions. Curr Pharm Des 19: 2174-2182.
-
(2013)
Curr Pharm Des
, vol.19
, pp. 2174-2182
-
-
Wang, J.-C.1
Lin, J.-H.2
-
160
-
-
0038266221
-
Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding
-
Wang J, Verkhivker GM (2003) Energy landscape theory, funnels, specificity, and optimal criterion of biomolecular binding. Phys Rev Lett 90: 188101.
-
(2003)
Phys Rev Lett
, vol.90
, pp. 188101
-
-
Wang, J.1
Verkhivker, G.M.2
-
161
-
-
0034811498
-
Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
-
Wang J, Morin P, Wang W, Kollman PA (2001) Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc 123: 5221-5230.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
162
-
-
0037763817
-
Comparative Evaluation of 11 Scoring Functions for Molecular Docking
-
doi:10.1021/jm0203783
-
Wang R, Lu Y, Wang S (2003) Comparative Evaluation of 11 Scoring Functions for Molecular Docking. J Med Chem 46: 2287-2303. doi: 10. 1021/jm0203783.
-
(2003)
J Med Chem
, vol.46
, pp. 2287-2303
-
-
Wang, R.1
Lu, Y.2
Wang, S.3
-
163
-
-
17144414125
-
Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA
-
doi:10.1021/jm049606e
-
Wang J, Kang X, Kuntz ID, Kollman PA (2005) Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. J Med Chem 48: 2432-2444. doi: 10. 1021/jm049606e.
-
(2005)
J Med Chem
, vol.48
, pp. 2432-2444
-
-
Wang, J.1
Kang, X.2
Kuntz, I.D.3
Kollman, P.A.4
-
164
-
-
0036922924
-
Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains
-
Weber J, Mesters JR, Lepsík M et al (2002) Unusual binding mode of an HIV-1 protease inhibitor explains its potency against multi-drug-resistant virus strains. J Mol Biol 324: 739-754.
-
(2002)
J Mol Biol
, vol.324
, pp. 739-754
-
-
Weber, J.1
Mesters, J.R.2
Lepsík, M.3
-
165
-
-
0030154893
-
Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites
-
Welch W, Ruppert J, Jain AN (1996) Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 3: 449-462.
-
(1996)
Chem Biol
, vol.3
, pp. 449-462
-
-
Welch, W.1
Ruppert, J.2
Jain, A.N.3
-
166
-
-
0041781898
-
Detailed analysis of grid-based molecular docking: A case study of CDOCKER?A CHARMm-based MD docking algorithm
-
doi:10.1002/jcc.10306
-
Wu G, Robertson DH, Brooks CL, Vieth M (2003) Detailed analysis of grid-based molecular docking: A case study of CDOCKER?A CHARMm-based MD docking algorithm. J Comput Chem 24: 1549-1562. doi: 10. 1002/jcc. 10306.
-
(2003)
J Comput Chem
, vol.24
, pp. 1549-1562
-
-
Wu, G.1
Robertson, D.H.2
Brooks, C.L.3
Vieth, M.4
-
167
-
-
77956034718
-
Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase - Ligand Interactions
-
doi:10.1021/ci100182c
-
Xue M, Zheng M, Xiong B et al (2010) Knowledge-Based Scoring Functions in Drug Design. 1. Developing a Target-Specific Method for Kinase - Ligand Interactions. J Chem Inf Model 50: 1378-1386. doi: 10. 1021/ci100182c.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 1378-1386
-
-
Xue, M.1
Zheng, M.2
Xiong, B.3
-
168
-
-
84859783507
-
Specificity quantification of biomolecular recognition and its implication for drug discovery
-
doi:10.1038/srep00309
-
Yan Z, Wang J (2012) Specificity quantification of biomolecular recognition and its implication for drug discovery. Sci Rep. doi: 10. 1038/srep00309.
-
(2012)
Sci Rep
-
-
Yan, Z.1
Wang, J.2
-
169
-
-
33749239216
-
M-Score: A Knowledge-Based Potential Scoring Function Accounting for Protein Atom Mobility
-
doi:10.1021/jm050043w
-
Yang C-Y, Wang R, Wang S (2006) M-Score: A Knowledge-Based Potential Scoring Function Accounting for Protein Atom Mobility. J Med Chem 49: 5903-5911. doi: 10. 1021/jm050043w.
-
(2006)
J Med Chem
, vol.49
, pp. 5903-5911
-
-
Yang, C.-Y.1
Wang, R.2
Wang, S.3
-
170
-
-
70349755625
-
Importance of Ligand Reorganization Free Energy in Protein - Ligand Binding-Affinity Prediction
-
doi:10.1021/ja9039373
-
Yang C-Y, Sun H, Chen J et al (2009) Importance of Ligand Reorganization Free Energy in Protein - Ligand Binding-Affinity Prediction. J Am Chem Soc 131: 13709-13721. doi: 10. 1021/ja9039373.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 13709-13721
-
-
Yang, C.-Y.1
Sun, H.2
Chen, J.3
-
171
-
-
84875480305
-
Latest developments in molecular docking: 2010-2011 in review
-
doi:10.1002/jmr.2266
-
Yuriev E, Ramsland PA (2013) Latest developments in molecular docking: 2010-2011 in review. J Mol Recognit JMR 26: 215-239. doi: 10. 1002/jmr. 2266.
-
(2013)
J Mol Recognit JMR
, vol.26
, pp. 215-239
-
-
Yuriev, E.1
Ramsland, P.A.2
-
172
-
-
0001147249
-
Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex
-
doi:10.1002/(SICI)1096-987X(199902)20:3<287::AID-JCC1>3.0.CO;2-H
-
Zacharias M, Sklenar H (1999) Harmonic modes as variables to approximately account for receptor flexibility in ligand-receptor docking simulations: Application to DNA minor groove ligand complex. J Comput Chem 20: 287-300. doi: 10. 1002/(SICI)1096-987X(199902)20: 3<287:: AID-JCC1>3. 0. CO;2-H.
-
(1999)
J Comput Chem
, vol.20
, pp. 287-300
-
-
Zacharias, M.1
Sklenar, H.2
-
173
-
-
0031552370
-
Determination of atomic desolvation energies from the structures of crystallized proteins
-
doi:10.1006/jmbi.1996.0859
-
Zhang C, Vasmatzis G, Cornette JL, DeLisi C (1997) Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 267: 707-726. doi: 10. 1006/jmbi. 1996. 0859.
-
(1997)
J Mol Biol
, vol.267
, pp. 707-726
-
-
Zhang, C.1
Vasmatzis, G.2
Cornette, J.L.3
DeLisi, C.4
-
174
-
-
34250892548
-
eHiTS: a new fast, exhaustive flexible ligand docking system
-
doi:10.1016/j.jmgm.2006.06.002
-
Zsoldos Z, Reid D, Simon A et al (2007) eHiTS: a new fast, exhaustive flexible ligand docking system. J Mol Graph Model 26: 198-212. doi: 10. 1016/j. jmgm. 2006. 06. 002.
-
(2007)
J Mol Graph Model
, vol.26
, pp. 198-212
-
-
Zsoldos, Z.1
Reid, D.2
Simon, A.3
|