-
4
-
-
11144323163
-
Virtual screening of chemical libraries
-
DOI 10.1038/nature03197
-
Shoichet BK (2004) Virtual screening of chemical libraries. Nature 432:862-865. (Pubitemid 40037142)
-
(2004)
Nature
, vol.432
, Issue.7019
, pp. 862-865
-
-
Shoichet, B.K.1
-
5
-
-
0036076470
-
Structure-based discovery of a novel, noncovalent inhibitor of AmpC β-lactamase
-
DOI 10.1016/S0969-2126(02)00799-2, PII S0969212602007992
-
Powers RA, Morandi F, Shoichet BK (2002) Structure-based discovery of a novel, noncovalent inhibitor of AmpC beta-lactamase. Structure 10:1013-1023. (Pubitemid 34786743)
-
(2002)
Structure
, vol.10
, Issue.7
, pp. 1013-1023
-
-
Powers, R.A.1
Morandi, F.2
Shoichet, B.K.3
-
6
-
-
0038798604
-
Nuclear hormone receptor targeted virtual screening
-
DOI 10.1021/jm0300173
-
Schapira M, Abagyan R, Totrov M (2003) Nuclear hormone receptor targeted virtual screening. J Med Chem 46:3045-3059. (Pubitemid 36775926)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.14
, pp. 3045-3059
-
-
Schapira, M.1
Abagyan, R.2
Totrov, M.3
-
7
-
-
3242884966
-
High-throughput docking as a source of novel drug leads
-
Alvarez JC (2004) High-throughput docking as a source of novel drug leads. Curr Opin Chem Biol 8:1-6.
-
(2004)
Curr Opin Chem Biol
, vol.8
, pp. 1-6
-
-
Alvarez, J.C.1
-
8
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz ID, Blaney JM, Oatley SJ et al (1982) A geometric approach to macromolecule-ligand interactions. J Mol Biol 161:269-288.
-
(1982)
J Mol Biol
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
-
9
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
DOI 10.1006/jmbi.1996.0897
-
Jones G, Willet P, Glen RC et al (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748. (Pubitemid 27170693)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.3
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
10
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
DOI 10.1006/jmbi.1996.0477
-
Rarey M, Kramer B, Lengauer Tet al (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-489. (Pubitemid 26335901)
-
(1996)
Journal of Molecular Biology
, vol.261
, Issue.3
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
11
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. I. 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. (Pubitemid 38380917)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.7
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
12
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
DOI 10.1021/jm980536j
-
Muegge I, Martin YC (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 42:791-804. (Pubitemid 29136170)
-
(1999)
Journal of Medicinal Chemistry
, vol.42
, Issue.5
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
13
-
-
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, Corkey JJ, Murcko MA et al (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. (Pubitemid 30020261)
-
(1999)
Journal of Medicinal Chemistry
, vol.42
, Issue.25
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
14
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
DOI 10.1002/prot.20088
-
Perola E, Walters WP, Charifson PS (2004) A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 56:235-249. (Pubitemid 38850158)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.2
, pp. 235-249
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.S.3
-
15
-
-
0035966871
-
Detailed analysis of scoring functions for virtual screening
-
DOI 10.1021/jm0003992
-
Stahl M, Rarey M (2001) Detailed analysis of scoring functions for virtual screening. J Med Chem 44:1035-1042. (Pubitemid 32852130)
-
(2001)
Journal of Medicinal Chemistry
, vol.44
, Issue.7
, pp. 1035-1042
-
-
Stahl, M.1
Rarey, M.2
-
16
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
Warren GL, Andrews CW, Capelli A-M et al (2006) A critical assessment of docking programs and scoring functions. J Med Chem 49:5912-5931. (Pubitemid 44484938)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.-M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
17
-
-
84961980685
-
Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
-
Kuhn B, Kollman PA (2000) Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J Med Chem 43:3786-3791.
-
(2000)
J Med Chem
, vol.43
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
18
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC et al (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112:6127-6129.
-
(1990)
J Am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
-
19
-
-
26944477331
-
Virtual ligand screening against Escherichia coli dihydrofolate reductase: Improving Docking enrichment using physics-based methods
-
DOI 10.1177/1087057105281220
-
Bernacki K, Kalyanaraman C, Jacobson MP (2005) Virtual Ligand Screening against Escherichia coli dihydrofolate reductase: Improving docking enrichment physics-based methods. J Biomol Screening 10:675-681. (Pubitemid 41476801)
-
(2005)
Journal of Biomolecular Screening
, vol.10
, Issue.7
, pp. 675-681
-
-
Bernacki, K.1
Kalyanaraman, C.2
Jacobson, M.P.3
-
20
-
-
33244490820
-
Physics-based scoring of protein - Ligand complexes: Enrichment of known inhibitors in large-scale virtual screening
-
DOI 10.1021/ci0502855
-
Huang N, Kalyanaraman C, Irwin JJ et al (2006) Physics-based scoring of proteinligand complexes: Enrichment of known inhibitors in large-scale virtual screening. J Chem Inf Model 46:243-253. (Pubitemid 43282119)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.1
, pp. 243-253
-
-
Huang, N.1
Kalyanaraman, C.2
Irwin, J.J.3
Jacobson, M.P.4
-
21
-
-
33750898990
-
Molecular mechanics methods for predicting protein-ligand binding
-
Huang N, Kalyanaraman C, Bernacki K et al (2006) Molecular mechanics methods for predicting protein-ligand binding. Phys Chem Chem Phys 8:5166-5177.
-
(2006)
Phys Chem Chem Phys
, vol.8
, pp. 5166-5177
-
-
Huang, N.1
Kalyanaraman, C.2
Bernacki, K.3
-
22
-
-
33746872935
-
Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring
-
DOI 10.1021/jm060522a
-
Lyne PD, Lamb ML, Saeh JC (2006) Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. J Med Chem 49:4805-4808. (Pubitemid 44201037)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.16
, pp. 4805-4808
-
-
Lyne, P.D.1
Lamb, M.L.2
Saeh, J.C.3
-
23
-
-
36148998422
-
Improving docking accuracy through molecular mechanics generalized Born optimization and scoring
-
Lee MR, Sun Y (2007) Improving docking accuracy through molecular mechanics generalized Born optimization and scoring. J Chem Theory Comput 3:1106-1119.
-
(2007)
J Chem Theory Comput
, vol.3
, pp. 1106-1119
-
-
Lee, M.R.1
Sun, Y.2
-
25
-
-
33845335781
-
Towards predictive ligand design with free-energy based computational methods?
-
DOI 10.2174/092986706779026165
-
Foloppe N, Hubbard R (2006) Towards predictive ligand design with free-energy based computational methods? Curr Med Chem 13:3583-3608. (Pubitemid 44873749)
-
(2006)
Current Medicinal Chemistry
, vol.13
, Issue.29
, pp. 3583-3608
-
-
Foloppe, N.1
Hubbard, R.2
Foloppe, N.3
-
26
-
-
28144441347
-
Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP Kinase
-
DOI 10.1021/jm050306m
-
Pearlman DA (2005) Evaluating the molecular mechanics Poisson-Boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase. J Med Chem 48:7796-807. (Pubitemid 41698819)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.24
, pp. 7796-7807
-
-
Pearlman, D.A.1
-
27
-
-
67650997041
-
Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using Glide
-
Kawatkar S, Wang H, Czerminski R et al (2009) Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using Glide. J Comput-Aided Mol Des 23:527-539.
-
(2009)
J Comput-Aided Mol des
, vol.23
, pp. 527-539
-
-
Kawatkar, S.1
Wang, H.2
Czerminski, R.3
-
28
-
-
45749138489
-
MM-GB/SA rescoring of docking poses in structure-based lead optimization
-
Guimarães CRW, Cardozo M (2008) MM-GB/SA rescoring of docking poses in structure-based lead optimization. J Chem Inf Model 48:958-970.
-
(2008)
J Chem Inf Model
, vol.48
, pp. 958-970
-
-
Guimarães, C.R.W.1
Cardozo, M.2
-
29
-
-
40949163431
-
Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
-
DOI 10.1021/ja0771033
-
Abel R, Young T, Farid R et al (2008) Role of the active-site solvent in the thermodynamics of Factor Xa ligand binding. J Am Chem Soc 130:2817-2831. (Pubitemid 351416242)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.9
, pp. 2817-2831
-
-
Abel, R.1
Young, T.2
Farid, R.3
Berne, B.J.4
Friesner, R.A.5
-
30
-
-
77951997162
-
Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free-energy perturbation calculations
-
Guimarães CRW, Mathiowetz AM (2010) Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free-energy perturbation calculations. J Chem Inf Model 50:547-559.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 547-559
-
-
Crw, G.1
Mathiowetz, A.M.2
-
31
-
-
0029912748
-
Development and testing of OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11235.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11235
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
32
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
DOI 10.1021/jp003919d
-
Kaminski GA, Friesner RA, Tirado-Rives J et al (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474-6487. (Pubitemid 35339015)
-
(2001)
Journal of Physical Chemistry B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
33
-
-
79956129180
-
-
Schrödinger LLC, New York, NY
-
MacroModel, version 9.8, Schrödinger, LLC, New York, NY, 2010.
-
(2010)
MacroModel, Version 9.8
-
-
-
34
-
-
77953760252
-
-
Schrödinger LLC, New York, NY
-
Maestro, version 9.1, Schrödinger, LLC, New York, NY, 2010.
-
(2010)
Maestro, Version 9.1
-
-
-
35
-
-
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. (Pubitemid 44595196)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.21
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
36
-
-
80052561956
-
-
Schrödinger LLC, New York, NY
-
Glide, version 5.6, Schrödinger, LLC, New York, NY, 2010.
-
(2010)
Glide, Version 5.6
-
-
-
38
-
-
0043162336
-
An internal coordinate Monte-Carlo method for searching conformational space
-
Chang G, Guida W, Still WC (1989) An internal coordinate Monte-Carlo method for searching conformational space. J Am Chem Soc 111:4379-4384.
-
(1989)
J Am Chem Soc
, vol.111
, pp. 4379-4384
-
-
Chang, G.1
Guida, W.2
Still, W.C.3
-
39
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
DOI 10.1021/jm049081q
-
Kuhn B, Gerber P, Schulz-Gasch, T et al (2005) Validation and use of the MM-PBSA approach for drug discovery. J Med Chem 48:4040-4048. (Pubitemid 40800612)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.12
, pp. 4040-4048
-
-
Kuhn, B.1
Gerber, P.2
Schulz-Gasch, T.3
Stahl, M.4
-
41
-
-
7044260905
-
Free energies of hydration from a generalized Born model and an all-atom force Field
-
Jorgensen WL, Ulmschneider JP, Tirado-Rives J (2004) Free energies of hydration from a generalized Born model and an all-atom force Field. J Phys Chem B 108:16264-16270.
-
(2004)
J Phys Chem B
, vol.108
, pp. 16264-16270
-
-
Jorgensen, W.L.1
Ulmschneider, J.P.2
Tirado-Rives, J.3
-
42
-
-
33847723384
-
Secondary structure bias in generalized born solvent models: Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation
-
DOI 10.1021/jp066831u
-
Roe DR, Okur A, Wickstrom L et al (2007) Secondary structure bias in generalized Born solvent models: Comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. J Phys Chem B 111:1846-1857. (Pubitemid 46384278)
-
(2007)
Journal of Physical Chemistry B
, vol.111
, Issue.7
, pp. 1846-1857
-
-
Roe, D.R.1
Okur, A.2
Wickstrom, L.3
Hornak, V.4
Simmerling, C.5
-
43
-
-
0034227795
-
Enthalpy-entropy and cavity decomposition of alkane hydration free energies:Numerical results and implications for theories of hydrophobic solvation
-
Gallicchio E, Kubo MM, Levy RM (2000) Enthalpy-entropy and cavity decomposition of alkane hydration free energies:Numerical results and implications for theories of hydrophobic solvation. J Phys Chem B 104:6271-628.
-
(2000)
J Phys Chem B
, vol.104
, pp. 6271-628
-
-
Gallicchio, E.1
Kubo, M.M.2
Levy, R.M.3
-
44
-
-
0034823225
-
The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers
-
DOI 10.1021/ja0057474
-
Pitera JW, van Gunsteren WF (2001) The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers. J Am Chem Soc 123:3163-3164. (Pubitemid 32879595)
-
(2001)
Journal of the American Chemical Society
, vol.123
, Issue.13
, pp. 3163-3164
-
-
Pitera, J.W.1
Van Gunsteren, W.F.2
-
46
-
-
77951995087
-
-
Schrödinger, LLC, New York, NY
-
KNIME, version 1.2, Schrödinger, LLC, New York, NY, 2008
-
(2008)
KNIME, Version 1.2
-
-
|