-
1
-
-
0035004409
-
Perspectives on factor Xa inhibition
-
Rai, R.; Sprengeler, P. A.; Elrod, K. C.; Young, W. B. Perspectives on Factor Xa Inhibition Curr. Med. Chem. 2001, 8, 101-119 (Pubitemid 32416446)
-
(2001)
Current Medicinal Chemistry
, vol.8
, Issue.2
, pp. 101-119
-
-
Rai, R.1
Sprengeler, P.A.2
Elrod, K.C.3
Young, W.B.4
-
2
-
-
0037142372
-
Design and quantitative structure-activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa
-
DOI 10.1021/jm0111346
-
Matter, H.; Defossa, E.; Heinelt, U.; Blohm, P.-M.; Schneider, D.; Müller, A.; Herok, S. I.; Schreuder, H.; Liesum, A.; Brachvogel, V.; Lönze, P.; Walser, A.; Al-Obeidi, F.; Wildgoose, P. Design and Quantitative Structure-Activity Relationship of 3-Amidinobenzyl-1 H -indole-2-carboxamides as Potent, Nonchiral, and Selective Inhibitors of Blood Coagulation Factor Xa J. Med. Chem. 2002, 45, 2749-2769 (Pubitemid 34632656)
-
(2002)
Journal of Medicinal Chemistry
, vol.45
, Issue.13
, pp. 2749-2769
-
-
Matter, H.1
Defossa, E.2
Heinelt, U.3
Blohm, P.-M.4
Schneider, D.5
Muller, A.6
Herok, S.7
Schreuder, H.8
Liesum, A.9
Brachvogel, V.10
Lonze, P.11
Walser, A.12
Al-Obeidi, F.13
Wildgoose, P.14
-
3
-
-
0346996360
-
Analyses of Activity for Factor Xa Inhibitors Based on Monte Carlo Simulations
-
DOI 10.1021/jm030288d
-
Ostrosky, D.; Udier-Blagovic, M.; Jorgensen, W. L. Analyses of Activity for Factor Xa Inhibitors Based on Monte Carlo Simulations J. Med. Chem. 2003, 46, 5691-5699 (Pubitemid 37543319)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.26
, pp. 5691-5699
-
-
Ostrovsky, D.1
Udier-Blagovic, M.2
Jorgensen, W.L.3
-
4
-
-
20444424191
-
Ligand-based assessment of factor Xa binding site flexibility via elaborate pharmacophore exploration and genetic algorithm-based QSAR modeling
-
DOI 10.1016/j.ejmech.2004.10.014, PII S0223523404002569
-
Taha, M. O.; Qandil, A. M.; Zaki, D. D.; AlDamen, M. A. Ligand-Based Assessment of Factor Xa Binding Site Flexibility via Elaborate Pharmacophore Exploration and Genetic Algorithm-Based QSAR Modeling Eur. J. Med. Chem. 2005, 40, 701-727 (Pubitemid 40797566)
-
(2005)
European Journal of Medicinal Chemistry
, vol.40
, Issue.7
, pp. 701-727
-
-
Taha, M.O.1
Qandil, A.M.2
Zaki, D.D.3
Aldamen, M.A.4
-
5
-
-
0026337077
-
The Coagulation Cascade: Initiation, Maintenance, and Regulation
-
Davie, E. W.; Fujikawa, K.; Kisiel, W. The Coagulation Cascade: Initiation, Maintenance, and Regulation Biochemistry 1991, 30, 10363-10370
-
(1991)
Biochemistry
, vol.30
, pp. 10363-10370
-
-
Davie, E.W.1
Fujikawa, K.2
Kisiel, W.3
-
6
-
-
74949139434
-
The New Oral Anticoagulants
-
Garcia, D.; Libby, E.; Crowther, M. A. The New Oral Anticoagulants Blood 2010, 115, 15-20
-
(2010)
Blood
, vol.115
, pp. 15-20
-
-
Garcia, D.1
Libby, E.2
Crowther, M.A.3
-
7
-
-
77950880770
-
Update on Antithrombotic Therapy. New Anticoagulants
-
Eikelboom, J. W.; Weitz, J. I. Update on Antithrombotic Therapy. New Anticoagulants Circulation 2010, 121, 1523-1532
-
(2010)
Circulation
, vol.121
, pp. 1523-1532
-
-
Eikelboom, J.W.1
Weitz, J.I.2
-
8
-
-
0037008160
-
Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
-
Gohlke, H.; Klebe, G. Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors Angew. Chem., Int. Ed. 2002, 41, 2644-2676
-
(2002)
Angew. Chem., Int. Ed.
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
9
-
-
33646471468
-
Statistical Mechanics of Fluid Mixtures
-
Kirkwood, J. G. Statistical Mechanics of Fluid Mixtures J. Chem. Phys. 1935, 3, 300-313
-
(1935)
J. Chem. Phys.
, vol.3
, pp. 300-313
-
-
Kirkwood, J.G.1
-
10
-
-
33646415982
-
Direct Calculation of the Binding Free Energies of FKBP Ligands
-
Fujitani, H.; Tanida, Y.; Ito, M.; Jayachandran, G.; Snow, C. D.; Shirts, M. R.; Sorin, E. J.; Pande, V. S. Direct Calculation of the Binding Free Energies of FKBP Ligands J. Chem. Phys. 2005, 123, 084108
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 084108
-
-
Fujitani, H.1
Tanida, Y.2
Ito, M.3
Jayachandran, G.4
Snow, C.D.5
Shirts, M.R.6
Sorin, E.J.7
Pande, V.S.8
-
11
-
-
33644532518
-
Can Free Energy Calculations Be Fast and Accurate at the Same Time? Binding of Low-Affinity, Non-Peptide Inhibitors to the SH2 Domain of the src Protein
-
Chipot, C.; Rozanska, X.; Dixit, S. B. Can Free Energy Calculations Be Fast and Accurate at the Same Time? Binding of Low-Affinity, Non-Peptide Inhibitors to the SH2 Domain of the src Protein J. Comput. Aided Mol. Design. 2005, 19, 765-770
-
(2005)
J. Comput. Aided Mol. Design.
, vol.19
, pp. 765-770
-
-
Chipot, C.1
Rozanska, X.2
Dixit, S.B.3
-
12
-
-
0342321950
-
Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease
-
Sham, Y. Y.; Chu, Z. T.; Tao, H.; Warshel, A. Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease Proteins: Struct Funct Genet 2000, 39, 393-407 (Pubitemid 30414177)
-
(2000)
Proteins: Structure, Function and Genetics
, vol.39
, Issue.4
, pp. 393-407
-
-
Sham, Y.Y.1
Chu, Z.T.2
Tao, H.3
Warshel, A.4
-
13
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Åqvist, J.; Medina, C.; Samuelsson, J. E. A New Method for Predicting Binding Affinity in Computer-Aided Drug Design Protein Eng. 1994, 7, 385-391 (Pubitemid 24063137)
-
(1994)
Protein Engineering
, vol.7
, Issue.3
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.-E.3
-
14
-
-
0032560959
-
Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices
-
Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices J. Am. Chem. Soc. 1998, 120, 9401-9809
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9809
-
-
Srinivasan, J.1
Cheatham III, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
15
-
-
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
-
16
-
-
77955653070
-
A Computational Analysis of the Binding Model of MDM2 with Inhibitors
-
Hu, G.; Wang, D.; Liu, X.; Zhang, A. A Computational Analysis of the Binding Model of MDM2 with Inhibitors J. Comput. Aided Mol. Des. 2010, 24, 687-697
-
(2010)
J. Comput. Aided Mol. Des.
, vol.24
, pp. 687-697
-
-
Hu, G.1
Wang, D.2
Liu, X.3
Zhang, A.4
-
17
-
-
39749152456
-
Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
-
DOI 10.1021/ja0779250
-
Stoica, I.; Sadiq, S. K.; Coveney, P. V. Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases J. Am. Chem. Soc. 2008, 130, 2639-2648 (Pubitemid 351304779)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.8
, pp. 2639-2648
-
-
Stoica, I.1
Sadiq, S.K.2
Coveney, P.V.3
-
18
-
-
0347602124
-
Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf
-
Gohlke, H.; Case, D. A. Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf J. Comput. Chem. 2003, 25, 238-250
-
(2003)
J. Comput. Chem.
, vol.25
, pp. 238-250
-
-
Gohlke, H.1
Case, D.A.2
-
19
-
-
77952786003
-
Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases
-
Sadiq, S. K.; Wright, D. W.; Kenway, O. A.; Coveney, P. V. Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases J. Chem. Inf. Model. 2010, 50, 890-905
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 890-905
-
-
Sadiq, S.K.1
Wright, D.W.2
Kenway, O.A.3
Coveney, P.V.4
-
20
-
-
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, D. A. Evaluating the Molecular Mechanics Poisson-Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase J. Med. Chem. 2005, 48, 7796-7807 (Pubitemid 41698819)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.24
, pp. 7796-7807
-
-
Pearlman, D.A.1
-
21
-
-
20444377245
-
Validation and use of the MM-PBSA approach for drug discovery
-
DOI 10.1021/jm049081q
-
Kuhn, B.; Greber, P.; Schulz-Gasch, T.; Stahl, M Validation and Use of the MM-PBSA Approach for Drug Discovery J. Med. Chem. 2005, 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
-
22
-
-
33750467966
-
Ligand affinities predicted with the MM/PBSA method: Dependence on the simulation method and the force field
-
DOI 10.1021/jm0608210
-
Weis, A.; Katebzadeh, K.; Söderhjelm, P.; Nilsson, I.; Ryde, U. Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field J. Med. Chem. 2006, 49, 6596-6606 (Pubitemid 44657454)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.22
, pp. 6596-6606
-
-
Weis, A.1
Katebzadeh, K.2
Soderhjelm, P.3
Nilsson, I.4
Ryde, U.5
-
23
-
-
58149327312
-
An Improved Method to Predict the Entropy Term with the MM/PBSA Approach
-
Kongsted, J.; Ryde, U. An Improved Method to Predict the Entropy Term with the MM/PBSA Approach J. Comput-Aided Mol. Design. 2009, 23, 63-71
-
(2009)
J. Comput-Aided Mol. Design.
, vol.23
, pp. 63-71
-
-
Kongsted, J.1
Ryde, U.2
-
24
-
-
76249085850
-
How to Obtain Statistically Converged MM/GBSA Results
-
Genheden, S.; Ryde, U. How To Obtain Statistically Converged MM/GBSA Results J. Comput. Chem. 2010, 31, 837-846
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 837-846
-
-
Genheden, S.1
Ryde, U.2
-
25
-
-
0141956086
-
Single-Step Perturbations to Calculate Free Energy Differences from Unphysical Reference States: Limits on Size, Flexibility, and Character
-
Oostenbrink, C.; van Gunsteren, W. F. Single-Step Perturbations to Calculate Free Energy Differences from Unphysical Reference States: Limits on Size, Flexibility, and Character J. Comput. Chem. 2003, 24, 1730-1739
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1730-1739
-
-
Oostenbrink, C.1
Van Gunsteren, W.F.2
-
26
-
-
1542398220
-
Sampling and convergence in free energy calculations of protein-ligand interactions: The binding of triphenoxypyridine derivatives to factor Xa and trypsin
-
DOI 10.1023/B:JCAM.0000017374.53591.32
-
Villa, A.; Zangi, R.; Pieffet, G.; Mark, A. E. Sampling and Convergence in Free Energy Calculations of Protein-Ligand Interactions: The Binding of Triphenoxypyridine Derivatives to Factor Xa and Trypsin J. Comput. Aided Mol. Des. 2003, 17, 673-686 (Pubitemid 38344470)
-
(2003)
Journal of Computer-Aided Molecular Design
, vol.17
, Issue.10
, pp. 673-686
-
-
Villa, A.1
Zangi, R.2
Pieffet, G.3
Mark, A.E.4
-
27
-
-
7444257387
-
Efficient evaluation of binding free energy using continuum electrostatics solvation
-
DOI 10.1021/jm049726m
-
Huang, D.; Cafisch, A. Efficient Evaluation of Binding Free Energy Using Continuum Electrostatics Solvation J. Med. Chem. 2004, 45, 5791-5797 (Pubitemid 39447274)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.23
, pp. 5791-5797
-
-
Huang, D.1
Caflisch, A.2
-
28
-
-
0033081482
-
Modelling of Factor Xa-inhibitor complexes: A computational flexible docking approach
-
DOI 10.1002/(S ICI)1097-01 34(1999 0201)34:2<17 3::AID-PRO T3>3.0.CO;2-F
-
Rao, M. S.; Olson, A. J. Modelling of Factor Xa-Inhibitor Complexes: A Computational Flexible Docking Approach Proteins 1999, 34, 173-183 (Pubitemid 29028803)
-
(1999)
Proteins: Structure, Function and Genetics
, vol.34
, Issue.2
, pp. 173-183
-
-
Rao, M.S.1
Olson, A.J.2
-
29
-
-
0842304437
-
Virtual Screening with Flexible Docking and COMBINE-Based Models. Application to a Series of Factor Xa Inhibitors
-
DOI 10.1021/jm030137a
-
Murcia, M.; Ortiz, A. R. Virtual Screening with Flexible Docking and Combine-Based Models. Application to a Series of Factor Xa Inhibitors J. Med. Chem. 2004, 47, 805-820 (Pubitemid 38176784)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.4
, pp. 805-820
-
-
Murcia, M.1
Ortiz, A.R.2
-
30
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
DOI 10.1023/A:1011115820450
-
Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: Search Strategies for Automated Molecular Docking of Flexible Molecule Databases J. Comput. Aided Mol. Des. 2001, 15, 411-428 (Pubitemid 32452109)
-
(2001)
Journal of Computer-Aided Molecular Design
, vol.15
, Issue.5
, pp. 411-428
-
-
Ewing, T.J.A.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
31
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179-5197
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
32
-
-
2942532422
-
Development and Testing of a General Amber Force Field
-
Wang, J. M.; Wolf, R. M.; Caldwell, K. 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.M.1
Wolf, R.M.2
Caldwell, K.W.3
Kollman, P.A.4
Case, D.A.5
-
33
-
-
3042524904
-
A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model
-
Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model J. Phys. Chem. 1993, 97, 10269-10280
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
34
-
-
84986492477
-
Atomic Charges Derived from Semiempirical Methods
-
Besler, B. H.; Merz, K. M.; Kollman, P. A. Atomic Charges Derived from Semiempirical Methods J. Comput. Chem. 1990, 11, 431-439
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 431-439
-
-
Besler, B.H.1
Merz, K.M.2
Kollman, P.A.3
-
35
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impley, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impley, R.W.4
Klein, M.L.5
-
36
-
-
36849077550
-
Nonlinear Scaling Schemes for Lennard-Jones Interactions in Free Energy Calculations
-
Steinbrecher, T.; Mobley, D. L.; Case, D. A. Nonlinear Scaling Schemes for Lennard-Jones Interactions in Free Energy Calculations J. Chem. Phys. 2007, 127, 214108
-
(2007)
J. Chem. Phys.
, vol.127
, pp. 214108
-
-
Steinbrecher, T.1
Mobley, D.L.2
Case, D.A.3
-
37
-
-
77955663115
-
Prediction of Protein-Ligand Binding Affinity by Free Energy Simulations: Assumptions, Pitfalls and Expectations
-
Michel, J.; Essex, J. W. Prediction of Protein-Ligand Binding Affinity by Free Energy Simulations: Assumptions, Pitfalls and Expectations J. Comput. Aided Mol. Des. 2010, 24, 639-658
-
(2010)
J. Comput. Aided Mol. Des.
, vol.24
, pp. 639-658
-
-
Michel, J.1
Essex, J.W.2
-
38
-
-
58049201323
-
-
University of California, San Francisco.
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Crowley, M.; Walker, R. C.; Zhang, W.; Merz, K. M.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossvary, I.; Wong, K.; F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Yang, L.; Tan, C.; Mongan, J.; Hornak, V.; Cui, G.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Kollman, P. A. Amber 10, University of California, San Francisco, 2008.
-
(2008)
Amber 10
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Crowley, M.8
Walker, R.C.9
Zhang, W.10
Merz, K.M.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossvary, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Yang, L.24
Tan, C.25
Mongan, J.26
Hornak, V.27
Cui, G.28
Mathews, D.H.29
Seetin, M.G.30
Sagui, C.31
Babin, V.32
Kollman, P.A.33
more..
-
39
-
-
78049265751
-
-
University of California, San Francisco.
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 11, University of California, San Francisco, 2010.
-
(2010)
AMBER 11
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, G.15
Kolossváry, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Wu, X.20
Brozell, S.R.21
Steinbrecher, T.22
Gohlke, H.23
Cai, Q.24
Ye, X.25
Wang, J.26
Hsieh, M.-J.27
Cui, G.28
Roe, D.R.29
Mathews, D.H.30
Seetin, M.G.31
Sagui, C.32
Babin, V.33
Luchko, T.34
Gusarov, S.35
Kovalenko, A.36
Kollman, P.A.37
more..
-
40
-
-
0347949637
-
Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy
-
Swanson, J. M. J.; Henchman, R. H.; McCammon, J. A. Revisiting Free Energy Calculations: A Theoretical Connection to MM/PBSA and Direct Calculation of the Association Free Energy Biophys. J. 2004, 86, 67-74 (Pubitemid 38067436)
-
(2004)
Biophysical Journal
, vol.86
, Issue.1
, pp. 67-74
-
-
Swanson, J.M.J.1
Henchman, R.H.2
McCammon, J.A.3
-
41
-
-
1842479952
-
Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
-
DOI 10.1002/prot.20033
-
Onufriev, A.; Bashford, D.; Case, D. A. Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model Proteins 2004, 55, 383-394 (Pubitemid 38437495)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.2
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
42
-
-
0035846166
-
Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
-
DOI 10.1021/jm0100279
-
Pearlman, D. A.; Charifson, P. S. Are free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 Map Kinase Protein System J. Med. Chem. 2001, 44, 3417-3423 (Pubitemid 32947908)
-
(2001)
Journal of Medicinal Chemistry
, vol.44
, Issue.21
, pp. 3417-3423
-
-
Pearlman, D.A.1
Charifson, P.S.2
-
43
-
-
0242509772
-
Self-Guided Langevin Dynamics Simulation Method
-
Wu, X.; Brooks, B. R. Self-Guided Langevin Dynamics Simulation Method Chem. Phys. Lett. 2003, 381, 512-518
-
(2003)
Chem. Phys. Lett.
, vol.381
, pp. 512-518
-
-
Wu, X.1
Brooks, B.R.2
-
44
-
-
33750587438
-
Molecular Dynamics with Coupling to an External Bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; DiNola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
45
-
-
33846823909
-
Particle Mesh Ewald: An N •log(N) Method for Ewald Sums in Large Systems
-
Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N •log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
46
-
-
33646940952
-
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n -Alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n -Alkanes J. Comput. Phys. 1977, 23, 327-341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
47
-
-
1542742143
-
Free Energy Simulations: Use of Reverse Cumulative Averaging to Determine the Equilibrated Region and the Time Required for Convergence
-
Yang, W.; Bitetti-Putzer, R.; Karplus, M. Free Energy Simulations: Use of Reverse Cumulative Averaging To Determine the Equilibrated Region and the Time Required for Convergence J. Chem. Phys. 2004, 120, 2618-2628
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 2618-2628
-
-
Yang, W.1
Bitetti-Putzer, R.2
Karplus, M.3
-
48
-
-
78149440040
-
A Comparison of Different Initialisation Protocols to Obtain Statistically Independent Molecular Dynamics Simulations
-
Genheden, S.; Ryde, U. A Comparison of Different Initialisation Protocols to Obtain Statistically Independent Molecular Dynamics Simulations J. Comput. Chem. 2011, 32, 187-195
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 187-195
-
-
Genheden, S.1
Ryde, U.2
-
49
-
-
33645400172
-
A Multistep Approach to Structure-Based Drug Design: Studying Ligand Binding at the Human Neutrophil Elastase
-
Steinbrecher, T.; Case, D. A.; Labahn, A. A Multistep Approach to Structure-Based Drug Design: Studying Ligand Binding at the Human Neutrophil Elastase J. Med. Chem. 2006, 49, 1837-1844
-
(2006)
J. Med. Chem.
, vol.49
, pp. 1837-1844
-
-
Steinbrecher, T.1
Case, D.A.2
Labahn, A.3
-
50
-
-
33845493850
-
Protein-Ligand Binding Affinity Predictions by Implicit Solvent Simulations: A Tool for Lead Optimization?
-
Michel, J.; Verdonk, M. L.; Essex, J. Protein-Ligand Binding Affinity Predictions by Implicit Solvent Simulations: A Tool for Lead Optimization? J. Med. Chem. 2006, 49, 7427-7539
-
(2006)
J. Med. Chem.
, vol.49
, pp. 7427-7539
-
-
Michel, J.1
Verdonk, M.L.2
Essex, J.3
-
51
-
-
65249136476
-
Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir
-
Lawrenz, M.; Baron, R.; McCammon, J. A. Independent-Trajectories Thermodynamic-Integration Free-Energy Changes for Biomolecular Systems: Determinants of H5N1 Avian Influenza Virus Neuraminidase Inhibition by Peramivir J. Chem. Theory Comput. 2009, 5, 1106-1116
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 1106-1116
-
-
Lawrenz, M.1
Baron, R.2
McCammon, J.A.3
-
52
-
-
11944270178
-
Cation- π Interactions: Nonadditive Effects Are Critical in Their Accurate Representation
-
Caldwell, J. W.; Kollman, P. A. Cation- π Interactions: Nonadditive Effects Are Critical in Their Accurate Representation J. Am. Chem. Soc. 1995, 117, 4177-4178
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4177-4178
-
-
Caldwell, J.W.1
Kollman, P.A.2
-
53
-
-
77953976984
-
An MM/3D-RISM Approach for Ligand-Binding Affinities
-
Genheden, S.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Ryde, U. An MM/3D-RISM Approach for Ligand-Binding Affinities J. Phys. Chem. B. 2010, 114, 8505-8516
-
(2010)
J. Phys. Chem. B.
, vol.114
, pp. 8505-8516
-
-
Genheden, S.1
Luchko, T.2
Gusarov, S.3
Kovalenko, A.4
Ryde, U.5
-
54
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated Docking Using a Lamarckian Genetic Algorithm and an Empirical Binding Free Energy Function J. Comput. Chem. 1998, 19, 1639-1662 (Pubitemid 128590223)
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.14
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
55
-
-
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
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