-
1
-
-
64749108083
-
Structure-Based Discovery of Dengue Virus Protease Inhibitors
-
Tomlinson, S. M.; Malmstrom, R. D.; Russo, A.; Mueller, N.; Pang, Y. P.; Watowich, S. J. Structure-Based Discovery of Dengue Virus Protease Inhibitors Antiviral Res. 2009, 82, 110-114
-
(2009)
Antiviral Res.
, vol.82
, pp. 110-114
-
-
Tomlinson, S.M.1
Malmstrom, R.D.2
Russo, A.3
Mueller, N.4
Pang, Y.P.5
Watowich, S.J.6
-
2
-
-
66349085848
-
Identification of a Novel Inhibitor of Jak2 Tyrosine Kinase by Structure-Based Virtual Screening
-
Kiss, R.; Polgar, T.; Kirabo, A.; Sayyah, J.; Figueroa, N. C.; List, A. F.; Sokol, L.; Zuckerman, K. S.; Gali, M.; Bisht, K. S.; Sayeski, P. P.; Keseru, G. M. Identification of a Novel Inhibitor of Jak2 Tyrosine Kinase by Structure-Based Virtual Screening Bioorg. Med. Chem. Lett. 2009, 19 (13) 3596-3601
-
(2009)
Bioorg. Med. Chem. Lett.
, vol.19
, Issue.13
, pp. 3596-3601
-
-
Kiss, R.1
Polgar, T.2
Kirabo, A.3
Sayyah, J.4
Figueroa, N.C.5
List, A.F.6
Sokol, L.7
Zuckerman, K.S.8
Gali, M.9
Bisht, K.S.10
Sayeski, P.P.11
Keseru, G.M.12
-
3
-
-
64249107125
-
Structure-Based Virtual Screening of Src Kinase Inhibitors
-
Lee, K.; Kim, J.; Jeong, K. W.; Lee, K. W.; Lee, Y.; Song, J. Y.; Kim, M. S.; Lee, G. S.; Kim, Y. Structure-Based Virtual Screening of Src Kinase Inhibitors Bioorg. Med. Chem. 2009, 17, 3152-3161
-
(2009)
Bioorg. Med. Chem.
, vol.17
, pp. 3152-3161
-
-
Lee, K.1
Kim, J.2
Jeong, K.W.3
Lee, K.W.4
Lee, Y.5
Song, J.Y.6
Kim, M.S.7
Lee, G.S.8
Kim, Y.9
-
4
-
-
77649196704
-
Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening
-
Ravindranathan, K. P.; Mandiyan, V.; Ekkati, A. R.; Bae, J. H.; Schlessinger, J.; Jorgensen, W. L. Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening J. Med. Chem. 2010, 53, 1662-1672
-
(2010)
J. Med. Chem.
, vol.53
, pp. 1662-1672
-
-
Ravindranathan, K.P.1
Mandiyan, V.2
Ekkati, A.R.3
Bae, J.H.4
Schlessinger, J.5
Jorgensen, W.L.6
-
5
-
-
77951974178
-
Identification of Potent Urease Inhibitors Via Ligand- and Structure-Based Virtual Screening and in Vitro Assays
-
Khan, K. M.; Wadood, A.; Ali, M.; Zia, U.; Ul-Haq, Z.; Lodhi, M. A.; Khan, M.; Perveen, S.; Choudhary, M. I. Identification of Potent Urease Inhibitors Via Ligand- and Structure-Based Virtual Screening and in Vitro Assays J. Mol. Graph. Model. 2010, 28, 792-798
-
(2010)
J. Mol. Graph. Model.
, vol.28
, pp. 792-798
-
-
Khan, K.M.1
Wadood, A.2
Ali, M.3
Zia, U.4
Ul-Haq, Z.5
Lodhi, M.A.6
Khan, M.7
Perveen, S.8
Choudhary, M.I.9
-
6
-
-
61849150037
-
Virtual Screening to Identify Lead Inhibitors for Bacterial Nad Synthetase (Nads)
-
Moro, W. B.; Yang, Z.; Kane, T. A.; Brouillette, C. G.; Brouillette, W. J. Virtual Screening to Identify Lead Inhibitors for Bacterial Nad Synthetase (Nads) Bioorg. Med. Chem. Lett. 2009, 19, 2001-2005
-
(2009)
Bioorg. Med. Chem. Lett.
, vol.19
, pp. 2001-2005
-
-
Moro, W.B.1
Yang, Z.2
Kane, T.A.3
Brouillette, C.G.4
Brouillette, W.J.5
-
7
-
-
76449120588
-
Discovery of 3-(4-Bromophenyl)-6-Nitrobenzo[1.3.2]Dithiazolium Ylide 1,1-Dioxide as a Novel Dual Cyclooxygenase/5-Lipoxygenase Inhibitor That Also Inhibits Tumor Necrosis Factor-Alpha Production
-
Chen, C. S.; Tan, C. M.; Huang, C. H.; Chang, L. C.; Wang, J. P.; Cheng, F. C.; Chern, J. W. Discovery of 3-(4-Bromophenyl)-6-Nitrobenzo[1.3.2] Dithiazolium Ylide 1,1-Dioxide as a Novel Dual Cyclooxygenase/5-Lipoxygenase Inhibitor That Also Inhibits Tumor Necrosis Factor-Alpha Production Bioorg. Med. Chem. 2010, 18, 597-604
-
(2010)
Bioorg. Med. Chem.
, vol.18
, pp. 597-604
-
-
Chen, C.S.1
Tan, C.M.2
Huang, C.H.3
Chang, L.C.4
Wang, J.P.5
Cheng, F.C.6
Chern, J.W.7
-
8
-
-
66449114449
-
Identification of Novel Serotonin 2c Receptor Ligands by Sequential Virtual Screening
-
Ahmed, A.; Choo, H.; Cho, Y. S.; Park, W. K.; Pae, A. N. Identification of Novel Serotonin 2c Receptor Ligands by Sequential Virtual Screening Bioorg. Med. Chem. 2009, 17, 4559-4568
-
(2009)
Bioorg. Med. Chem.
, vol.17
, pp. 4559-4568
-
-
Ahmed, A.1
Choo, H.2
Cho, Y.S.3
Park, W.K.4
Pae, A.N.5
-
9
-
-
57749094583
-
Identification of Small Molecules That Inhibit Gsk-3beta through Virtual Screening
-
Kang, N. S.; Lee, G. N.; Kim, C. H.; Bae, M. A.; Kim, I.; Cho, Y. S. Identification of Small Molecules That Inhibit Gsk-3beta through Virtual Screening Bioorg. Med. Chem. Lett. 2009, 19, 533-537
-
(2009)
Bioorg. Med. Chem. Lett.
, vol.19
, pp. 533-537
-
-
Kang, N.S.1
Lee, G.N.2
Kim, C.H.3
Bae, M.A.4
Kim, I.5
Cho, Y.S.6
-
10
-
-
0035976367
-
EUDOC: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
-
DOI 10.1002/jcc.1129
-
Pang, Y. P.; Perola, E.; Xu, K.; Prendergast, F. G. Eudoc: A Computer Program for Identification of Drug Interaction Sites in Macromolecules and Drug Leads from Chemical Databases J. Comput. Chem. 2001, 22, 1750-1771 (Pubitemid 33044777)
-
(2001)
Journal of Computational Chemistry
, vol.22
, Issue.15
, pp. 1750-1771
-
-
Pang, Y.-P.1
Perola, E.2
Xu, R.3
Prendergast, F.G.4
-
11
-
-
33845873363
-
Development and validation of a modular, extensible docking program: DOCK 5
-
DOI 10.1007/s10822-006-9060-4
-
Moustakas, D. T.; Lang, P. T.; Pegg, S.; Pettersen, E.; Kuntz, I. D.; Brooijmans, N.; Rizzo, R. C. Development and Validation of a Modular, Extensible Docking Program: Dock 5 J. Comput.-Aided Mol. Des. 2006, 20, 601-619 (Pubitemid 46023925)
-
(2006)
Journal of Computer-Aided Molecular Design
, vol.20
, Issue.10-11
, pp. 601-619
-
-
Moustakas, D.T.1
Lang, P.T.2
Pegg, S.3
Pettersen, E.4
Kuntz, I.D.5
Brooijmans, N.6
Rizzo, R.C.7
-
12
-
-
12144289984
-
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
-
DOI 10.1021/jm0306430
-
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy J. Med. Chem. 2004, 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
-
13
-
-
34250681353
-
Detailed comparison of the protein-ligand docking efficiencies of GOLD, a commercial package and arguslab, a licensable freeware
-
Joy, S.; Nair, P. S.; Hariharan, R.; Pillai, M. R. Detailed Comparison of the Protein-Ligand Docking Efficiencies of Gold, a Commercial Package and Arguslab, a Licensable Freeware In Silico Biol. 2006, 6, 601-605 (Pubitemid 47028648)
-
(2006)
In Silico Biology
, vol.6
, Issue.6
, pp. 601-605
-
-
Joy, S.1
Nair, P.S.2
Hariharan, R.3
Pillai, M.R.4
-
14
-
-
0032738842
-
Evaluation of the FlexX incremental construction algorithm for protein- ligand docking
-
DOI 10.1002/(SICI)1097-0134(19991101)37:2<228::AID-PROT8>3.0.CO;2-8
-
Kramer, B.; Rarey, M.; Lengauer, T. Evaluation of the Flexx Incremental Construction Algorithm for Protein-Ligand Docking Proteins 1999, 37, 228-241 (Pubitemid 29503004)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.37
, Issue.2
, pp. 228-241
-
-
Kramer, B.1
Rarey, M.2
Lengauer, T.3
-
15
-
-
33947716119
-
Software news and update a semiempirical free energy force field with charge-based desolvation
-
DOI 10.1002/jcc.20634
-
Huey, R.; Morris, G. M.; Olson, A. J.; Goodsell, D. S. A Semiempirical Free Energy Force Field with Charge-Based Desolvation J. Comput. Chem. 2007, 28, 1145-1152 (Pubitemid 46506716)
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.6
, pp. 1145-1152
-
-
Huey, R.1
Morris, G.M.2
Olson, A.J.3
Goodsell, D.S.4
-
16
-
-
33744551693
-
Structure-based virtual screening of chemical libraries for drug discovery
-
DOI 10.1016/j.cbpa.2006.04.002, PII S1367593106000536
-
Ghosh, S.; Nie, A.; An, J.; Huang, Z. Structure-Based Virtual Screening of Chemical Libraries for Drug Discovery Curr. Opin. Chem. Biol. 2006, 10, 194-202 (Pubitemid 43815778)
-
(2006)
Current Opinion in Chemical Biology
, vol.10
, Issue.3
, pp. 194-202
-
-
Ghosh, S.1
Nie, A.2
An, J.3
Huang, Z.4
-
18
-
-
0036606483
-
Principles of docking: An overview of search algorithms and a guide to scoring functions
-
DOI 10.1002/prot.10115
-
Halperin, I.; Ma, B.; Wolfson, H.; Nussinov, R. Principles of Docking: An Overview of Search Algorithms and a Guide to Scoring Functions Proteins 2002, 47, 409-443 (Pubitemid 34614722)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.47
, Issue.4
, pp. 409-443
-
-
Halperin, I.1
Ma, B.2
Wolfson, H.3
Nussinov, R.4
-
19
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: Methods and applications
-
DOI 10.1038/nrd1549
-
Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and Scoring in Virtual Screening for Drug Discovery: Methods and Applications Nat. Rev. Drug Discovery 2004, 3, 935-949 (Pubitemid 39529931)
-
(2004)
Nature Reviews Drug Discovery
, vol.3
, Issue.11
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
20
-
-
33749245117
-
Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
-
DOI 10.1021/jm060999m
-
Leach, A. R.; Shoichet, B. K.; Peishoff, C. E. Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps J. Med. Chem. 2006, 49, 5851-5855 (Pubitemid 44484931)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5851-5855
-
-
Leach, A.R.1
Shoichet, B.K.2
Peishoff, C.E.3
-
21
-
-
1842431537
-
Comparative study of several algorithms for flexible ligand docking
-
DOI 10.1023/B:JCAM.0000017496.76572.6f
-
Bursulaya, B. D.; Totrov, M.; Abagyan, R.; Brooks, C. L., 3rd Comparative Study of Several Algorithms for Flexible Ligand Docking J. Comput.-Aided Mol. Des. 2003, 17, 755-763 (Pubitemid 38418287)
-
(2003)
Journal of Computer-Aided Molecular Design
, vol.17
, Issue.11
, pp. 755-763
-
-
Bursulaya, B.D.1
Totrov, M.2
Abagyan, R.3
Brooks III, C.L.4
-
22
-
-
13944263886
-
Comparison of automated docking programs as virtual screening tools
-
DOI 10.1021/jm049798d
-
Cummings, M. D.; DesJarlais, R. L.; Gibbs, A. C.; Mohan, V.; Jaeger, E. P. Comparison of Automated Docking Programs as Virtual Screening Tools J. Med. Chem. 2005, 48, 962-976 (Pubitemid 40270442)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.4
, pp. 962-976
-
-
Cummings, M.D.1
DesJarlais, R.L.2
Gibbs, A.C.3
Mohan, V.4
Jaeger, E.P.5
-
23
-
-
11144255694
-
Evaluation of library ranking efficacy in virtual screening
-
DOI 10.1002/jcc.20141
-
Kontoyianni, M.; Sokol, G. S.; McClellan, L. M. Evaluation of Library Ranking Efficacy in Virtual Screening J. Comput. Chem. 2005, 26, 11-22 (Pubitemid 40021619)
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.1
, pp. 11-22
-
-
Kontoyianni, M.1
Sokol, G.S.2
Mcclellan, L.M.3
-
24
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions J. Med. Chem. 2006, 49, 5912-5931 (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
-
25
-
-
0033576680
-
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
-
DOI 10.1021/jm990352k
-
Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins J. Med. Chem. 1999, 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
-
26
-
-
0036136868
-
Consensus scoring for ligand/protein interactions
-
DOI 10.1016/S1093-3263(01)00125-5, PII S1093326301001255
-
Clark, R. D.; Strizhev, A.; Leonard, J. M.; Blake, J. F.; Matthew, J. B. Consensus Scoring for Ligand/Protein Interactions J. Mol. Graph. Model. 2002, 20, 281-295 (Pubitemid 34017546)
-
(2002)
Journal of Molecular Graphics and Modelling
, vol.20
, Issue.4
, pp. 281-295
-
-
Clark, R.D.1
Strizhev, A.2
Leonard, J.M.3
Blake, J.F.4
Matthew, J.B.5
-
27
-
-
72449144245
-
Drug Efficiency Indices for Improvement of Molecular Docking Scoring Functions
-
Garcia-Sosa, A. T.; Hetenyi, C.; Maran, U. Drug Efficiency Indices for Improvement of Molecular Docking Scoring Functions J. Comput. Chem. 2009, 31, 174-184
-
(2009)
J. Comput. Chem.
, vol.31
, pp. 174-184
-
-
Garcia-Sosa, A.T.1
Hetenyi, C.2
Maran, U.3
-
28
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review Biophys. J. 1997, 72, 1047-1069 (Pubitemid 27113632)
-
(1997)
Biophysical Journal
, vol.72
, Issue.3
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
29
-
-
0035665229
-
The linear interaction energy method for predicting ligand binding free energies
-
Aqvist, J.; Marelius, J. The Linear Interaction Energy Method for Predicting Ligand Binding Free Energies Comb. Chem. High Throughput Screen. 2001, 4, 613-626 (Pubitemid 34003156)
-
(2001)
Combinatorial Chemistry and High Throughput Screening
, vol.4
, Issue.8
, pp. 613-626
-
-
Aqvist, J.1
Marelius, J.2
-
30
-
-
0034521981
-
Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
-
DOI 10.1021/ar000033j
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E., III. Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models Acc. Chem. Res. 2000, 33, 889-897 (Pubitemid 32056774)
-
(2000)
Accounts of Chemical Research
, vol.33
, Issue.12
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
-
31
-
-
0032054675
-
Computational alchemy to calculate absolute protein-Ligand binding free energy
-
DOI 10.1021/ja9738539
-
Helms, V.; Wade, R. Computational Alchemy to Calculate Absolute Protein-Ligand Binding Free Energy J. Am. Chem. Soc. 1998, 120, 2710-2713 (Pubitemid 28191625)
-
(1998)
Journal of the American Chemical Society
, vol.120
, Issue.12
, pp. 2710-2713
-
-
Helms, V.1
Wade, R.C.2
-
32
-
-
36549092795
-
Efficient Computation of Absolute Free-Energies of Binding by Computer-Simulations-Application to the Methane Dimer in Water
-
Jorgensen, W. L.; Buckner, J. K.; Boudon, S.; Tiradorives, J. Efficient Computation of Absolute Free-Energies of Binding by Computer-Simulations- Application to the Methane Dimer in Water J. Chem. Phys. 1988, 89, 3742-3746
-
(1988)
J. Chem. Phys.
, vol.89
, pp. 3742-3746
-
-
Jorgensen, W.L.1
Buckner, J.K.2
Boudon, S.3
Tiradorives, J.4
-
33
-
-
0141682863
-
Absolute Binding Free Energies: A Quantitative Approach for Their Calculation
-
Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. Absolute Binding Free Energies: A Quantitative Approach for Their Calculation J. Phys. Chem. B 2003, 107, 9535-9551
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 9535-9551
-
-
Boresch, S.1
Tettinger, F.2
Leitgeb, M.3
Karplus, M.4
-
34
-
-
33749238080
-
Calculation of Standard Binding Free Energies: Aromatic Molecules in T4 Lysozyme L99a Mutant
-
Deng, Y.; Roux, B. Calculation of Standard Binding Free Energies: Aromatic Molecules in T4 Lysozyme L99a Mutant J. Chem. Theory Comput. 2006, 2, 1225-1273
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1225-1273
-
-
Deng, Y.1
Roux, B.2
-
35
-
-
41049115037
-
Computation of Binding Free Energy with Molecular Dynamics and Grand Canonical Monte Carlo Simulations
-
Deng, Y.; Roux, B. Computation of Binding Free Energy with Molecular Dynamics and Grand Canonical Monte Carlo Simulations J. Chem. Phys. 2008, 128, 115103
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 115103
-
-
Deng, Y.1
Roux, B.2
-
36
-
-
33749532284
-
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials
-
DOI 10.1529/biophysj.106.084301
-
Wang, J.; Deng, Y.; Roux, B. Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials Biophys. J. 2006, 91, 2798-2814 (Pubitemid 44526470)
-
(2006)
Biophysical Journal
, vol.91
, Issue.8
, pp. 2798-2814
-
-
Wang, J.1
Deng, Y.2
Roux, B.3
-
37
-
-
65249124122
-
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
-
Deng, Y.; Roux, B. Computations of Standard Binding Free Energies with Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113, 2234-2246
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 2234-2246
-
-
Deng, Y.1
Roux, B.2
-
38
-
-
67650663433
-
New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors
-
Tomlinson, S. M.; Malmstrom, R. D.; Watowich, S. J. New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors Infect. Disord.: Drug Targets 2009, 9, 327-343
-
(2009)
Infect. Disord.: Drug Targets
, vol.9
, pp. 327-343
-
-
Tomlinson, S.M.1
Malmstrom, R.D.2
Watowich, S.J.3
-
39
-
-
0029016268
-
Energetic Origins of Specificity of Ligand Binding in an Interior Nonpolar Cavity of T4 Lysozyme
-
Morton, A.; Baase, W. A.; Matthews, B. W. Energetic Origins of Specificity of Ligand Binding in an Interior Nonpolar Cavity of T4 Lysozyme Biochemistry 1995, 34, 8564-8575
-
(1995)
Biochemistry
, vol.34
, pp. 8564-8575
-
-
Morton, A.1
Baase, W.A.2
Matthews, B.W.3
-
40
-
-
70349932423
-
Autodock4 and Autodocktools4: Automated Docking with Selective Receptor Flexibility
-
Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. Autodock4 and Autodocktools4: Automated Docking with Selective Receptor Flexibility J. Comput. Chem. 2009, 30, 2785-2791
-
(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
-
41
-
-
28044463816
-
Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation
-
DOI 10.1073/pnas.0508224102
-
Collins, M. D.; Hummer, G.; Quillin, M. L.; Matthews, B. W.; Gruner, S. M. Cooperative Water Filling of a Nonpolar Protein Cavity Observed by High-Pressure Crystallography and Simulation Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 16668-16671 (Pubitemid 41688834)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.46
, pp. 16668-16671
-
-
Collins, M.D.1
Hummer, G.2
Quillin, M.L.3
Matthews, B.W.4
Gruner, S.M.5
-
42
-
-
0029067489
-
Specificity of Ligand Binding in a Buried Nonpolar Cavity of T4 Lysozyme: Linkage of Dynamics and Structural Plasticity
-
Morton, A.; Matthews, B. W. Specificity of Ligand Binding in a Buried Nonpolar Cavity of T4 Lysozyme: Linkage of Dynamics and Structural Plasticity Biochemistry 1995, 34, 8576-8588
-
(1995)
Biochemistry
, vol.34
, pp. 8576-8588
-
-
Morton, A.1
Matthews, B.W.2
-
44
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
DOI 10.1016/j.jmgm.2005.12.005, PII S1093326305001737
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic Atom Type and Bond Type Perception in Molecular Mechanical Calculations J. Mol. Graph. Model. 2006, 25, 247-260 (Pubitemid 44363172)
-
(2006)
Journal of Molecular Graphics and Modelling
, vol.25
, Issue.2
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
45
-
-
2942532422
-
Development and Testing of a General Amber Force Field
-
Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and Testing of a General Amber Force Field J. Comput. Chem. 2004, 25, 1157-1174
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
46
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
DOI 10.1002/jcc.10128
-
Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. Am1-Bcc Model: Ii. Parameterization and Validation J. Comput. Chem. 2002, 23, 1623-1641 (Pubitemid 35330860)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.16
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
47
-
-
84986512474
-
Charmm: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, D. J.; States, D. J.; Swaminathan, S.; Karplus, M. Charmm: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations J. Comput. Chem. 1983, 4, 187-217
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, D.J.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
48
-
-
0000224283
-
-
In; John Wiley & Sons: Chichester:
-
MacKerel, Jr, A. D.; Brooks Iii, C. L.; Nilsson, L.; Roux, B.; Won, Y.; Karplus, M. In Charmm: The Energy Function and Its Parameterization with an Overview of the Program; John Wiley & Sons: Chichester: 1998; Vol. 1, pp 271-277.
-
(1998)
Charmm: The Energy Function and Its Parameterization with An Overview of the Program
, vol.1
, pp. 271-277
-
-
MacKerel, Jr.A.D.1
Brooks Iii, C.L.2
Nilsson, L.3
Roux, B.4
Won, Y.5
Karplus, M.6
-
49
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616 (Pubitemid 128576688)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
50
-
-
3142714765
-
Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations
-
Mackerell, A. D.; Feig, M.; Brooks, C. L., III. Extending the Treatment of Backbone Energetics in Protein Force Fields: Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations J. Comput. Chem. 2004, 25, 1400-1415
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
MacKerell, A.D.1
Feig, M.2
Brooks III, C.L.3
-
51
-
-
0000020246
-
A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid, Nonpolarizable Potential Functions
-
Mahoney, M. W.; Jorgensen, W. L. A Five-Site Model for Liquid Water and the Reproduction of the Density Anomaly by Rigid, Nonpolarizable Potential Functions J. Chem. Phys. 2000, 112, 8910-8922
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 8910-8922
-
-
Mahoney, M.W.1
Jorgensen, W.L.2
-
52
-
-
0026509036
-
A Cavity-Containing Mutant of T4 Lysozyme Is Stabilized by Buried Benzene
-
Eriksson, A. E.; Baase, W. A.; Wozniak, J. A.; Matthews, B. W. A Cavity-Containing Mutant of T4 Lysozyme Is Stabilized by Buried Benzene Nature 1992, 355, 371-373
-
(1992)
Nature
, vol.355
, pp. 371-373
-
-
Eriksson, A.E.1
Baase, W.A.2
Wozniak, J.A.3
Matthews, B.W.4
-
53
-
-
34547110591
-
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
-
DOI 10.1016/j.jmb.2007.06.002, PII S0022283607007760
-
Mobley, D. L.; Graves, A. P.; Chodera, J. D.; McReynolds, A. C.; Shoichet, B. K.; Dill, K. A. Predicting Absolute Ligand Binding Free Energies to a Simple Model Site J. Mol. Biol. 2007, 371, 1118-1134 (Pubitemid 47101818)
-
(2007)
Journal of Molecular Biology
, vol.371
, Issue.4
, pp. 1118-1134
-
-
Mobley, D.L.1
Graves, A.P.2
Chodera, J.D.3
McReynolds, A.C.4
Shoichet, B.K.5
Dill, K.A.6
-
54
-
-
0041989635
-
Conformational flexibility models for the receptor in structure based drug design
-
DOI 10.2174/1381612033454595
-
Teodoro, M. L.; Kavraki, L. E. Conformational Flexibility Models for the Receptor in Structure Based Drug Design Curr. Pharm. Des. 2003, 9, 1635-1648 (Pubitemid 36966031)
-
(2003)
Current Pharmaceutical Design
, vol.9
, Issue.20
, pp. 1635-1648
-
-
Teodoro, M.L.1
Kavraki, L.E.2
-
55
-
-
41949132916
-
Flexible Ligand Docking to Multiple Receptor Conformations: A Practical Alternative
-
Totrov, M.; Abagyan, R. Flexible Ligand Docking to Multiple Receptor Conformations: A Practical Alternative Curr. Opin. Struct. Biol. 2008, 18, 178-184
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
56
-
-
33747200808
-
Combining docking and molecular dynamic simulations in drug design
-
DOI 10.1002/med.20067
-
Alonso, H.; Bliznyuk, A. A.; Gready, J. E. Combining Docking and Molecular Dynamic Simulations in Drug Design Med. Res. Rev. 2006, 26, 531-568 (Pubitemid 44230412)
-
(2006)
Medicinal Research Reviews
, vol.26
, Issue.5
, pp. 531-568
-
-
Alonso, H.1
Bliznyuk, A.A.2
Gready, J.E.3
-
57
-
-
36049017659
-
The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change
-
Mobley, D. L.; Chodera, J. D.; Dill, K. A. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change J. Chem. Theory Comput. 2007, 3, 1231-1235
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1231-1235
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
-
58
-
-
34547110591
-
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
-
DOI 10.1016/j.jmb.2007.06.002, PII S0022283607007760
-
Mobley, D. L.; Graves, A. P.; Chodera, J. D.; McReynolds, A. C.; Shoichet, B. K.; Dill, K. A. Predicting Absolute Ligand Binding Free Energies to a Simple Model Site J. Mol. Biol. 2007, 371, 1118-1134 (Pubitemid 47101818)
-
(2007)
Journal of Molecular Biology
, vol.371
, Issue.4
, pp. 1118-1134
-
-
Mobley, D.L.1
Graves, A.P.2
Chodera, J.D.3
McReynolds, A.C.4
Shoichet, B.K.5
Dill, K.A.6
-
59
-
-
33748252631
-
On the Use of Orientational Restraints and Symmetry Corrections in Alchemical Free Energy Calculations
-
Mobley, D. L.; Chodera, J. D.; Dill, K. A. On the Use of Orientational Restraints and Symmetry Corrections in Alchemical Free Energy Calculations J. Chem. Phys. 2006, 125, 084902
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 084902
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
|