-
1
-
-
33947397110
-
Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent
-
Mobley, D. L.; Dumont, E.; Chodera, J. D.; Dill, K. A. Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent J. Phys. Chem. B 2007, 111, 2242-2254
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 2242-2254
-
-
Mobley, D.L.1
Dumont, E.2
Chodera, J.D.3
Dill, K.A.4
-
2
-
-
0001442195
-
Solvation free energies of amides and amines: Disagreement between free energy calculations and experiment
-
Morgantini, P.-Y.; Kollman, P. A. Solvation free energies of amides and amines: Disagreement between free energy calculations and experiment J. Am. Chem. Soc. 2002, 117, 6057-6063
-
(2002)
J. Am. Chem. Soc.
, vol.117
, pp. 6057-6063
-
-
Morgantini, P.-Y.1
Kollman, P.A.2
-
3
-
-
65249147164
-
Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model
-
Shivakumar, D.; Deng, Y.; Röux, B. Computations of absolute solvation free energies of small molecules using explicit and implicit solvent model J. Chem. Theory Comput. 2009, 5, 919-930
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 919-930
-
-
Shivakumar, D.1
Deng, Y.2
Röux, B.3
-
4
-
-
0032939345
-
Ligand solvation in molecular docking
-
Shoichet, B. K.; Leach, A. R.; Kuntz, I. D. Ligand solvation in molecular docking Proteins: Struct., Funct., Genet. 1999, 34, 4-16
-
(1999)
Proteins: Struct., Funct., Genet.
, vol.34
, pp. 4-16
-
-
Shoichet, B.K.1
Leach, A.R.2
Kuntz, I.D.3
-
5
-
-
3142707941
-
Accuracy of free energies of hydration using cm1 and cm3 atomic charges
-
Udier-Blagovic, M.; Morales, D. T. P.; Pearlman, S. A.; Jorgensen, W. L. Accuracy of free energies of hydration using cm1 and cm3 atomic charges J. Comput. Chem. 2004, 25, 1322-1332
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1322-1332
-
-
Udier-Blagovic, M.1
Morales, D.T.P.2
Pearlman, S.A.3
Jorgensen, W.L.4
-
6
-
-
77952415408
-
Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field
-
Shivakumar, D.; Williams, J.; Wu, Y.; Damm, W.; Shelley, J.; Sherman, W. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field J. Chem. Theory Comput. 2010, 6, 1509-1519
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1509-1519
-
-
Shivakumar, D.1
Williams, J.2
Wu, Y.3
Damm, W.4
Shelley, J.5
Sherman, W.6
-
7
-
-
0000433639
-
Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials
-
Gao, J. Absolute free energy of solvation from Monte Carlo simulations using combined quantum and molecular mechanical potentials J. Phys. Chem. 1992, 96, 537-540
-
(1992)
J. Phys. Chem.
, vol.96
, pp. 537-540
-
-
Gao, J.1
-
8
-
-
39749178969
-
Predicting small-molecule solvation free energies: An informal blind test for computational chemistry
-
Nicholls, A.; Mobley, D. L.; Guthrie, J. P.; Chodera, J. D.; Bayly, C. I.; Cooper, M. D.; Pande, V. S. Predicting small-molecule solvation free energies: An informal blind test for computational chemistry J. Med. Chem. 2008, 51, 769-779
-
(2008)
J. Med. Chem.
, vol.51
, pp. 769-779
-
-
Nicholls, A.1
Mobley, D.L.2
Guthrie, J.P.3
Chodera, J.D.4
Bayly, C.I.5
Cooper, M.D.6
Pande, V.S.7
-
9
-
-
79953005073
-
Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method
-
Bruckner, S.; Boresch, S. Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method J. Comput. Chem. 2011, 32, 1303-1319
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 1303-1319
-
-
Bruckner, S.1
Boresch, S.2
-
10
-
-
77955568818
-
Practically efficient QM/MM alchemical free energy simulations: The orthogonal space random walk strategy
-
Min, D.; Zheng, L.; Harris, W.; Chen, M.; Lv, C.; Yang, W. Practically efficient QM/MM alchemical free energy simulations: The orthogonal space random walk strategy J. Chem. Theory Comput. 2010, 6, 2253-2266
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2253-2266
-
-
Min, D.1
Zheng, L.2
Harris, W.3
Chen, M.4
Lv, C.5
Yang, W.6
-
11
-
-
79957593685
-
New theoretical method for rapid prediction of solvation free energy in water
-
Zhao, S.; Jin, Z.; Wu, J. New theoretical method for rapid prediction of solvation free energy in water J. Phys. Chem. B 2011, 115, 6971-6975
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 6971-6975
-
-
Zhao, S.1
Jin, Z.2
Wu, J.3
-
12
-
-
77957190340
-
End-point calculation of solvation free energy of amino-acid analogs by molecular theories of solution
-
Karino, Y.; Fedorov, M. V.; Matubayasi, N. End-point calculation of solvation free energy of amino-acid analogs by molecular theories of solution Chem. Phys. Lett. 2010, 496, 351-355
-
(2010)
Chem. Phys. Lett.
, vol.496
, pp. 351-355
-
-
Karino, Y.1
Fedorov, M.V.2
Matubayasi, N.3
-
13
-
-
80052785878
-
Small molecule solvation free energy: Enhanced conformational sampling using expanded ensemble molecular dynamics simulation
-
Paluch, A. S.; Mobley, D. L.; Maginn, E. J. Small molecule solvation free energy: Enhanced conformational sampling using expanded ensemble molecular dynamics simulation J. Chem. Theory Comput. 2011, 7, 2910-2918
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2910-2918
-
-
Paluch, A.S.1
Mobley, D.L.2
Maginn, E.J.3
-
14
-
-
79960164079
-
Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions
-
Lin, B.; Wong, K.-Y.; Hu, C.; Kokubo, H.; Pettitt, B. M. Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions J. Phys. Chem. Lett. 2011, 2, 1626-1632
-
(2011)
J. Phys. Chem. Lett.
, vol.2
, pp. 1626-1632
-
-
Lin, B.1
Wong, K.-Y.2
Hu, C.3
Kokubo, H.4
Pettitt, B.M.5
-
15
-
-
77952388331
-
Rapid prediction of solvation free energy. 1. An extensive test of linear interaction energy (LIE)
-
Sulea, T.; Corbeil, C. R.; Purisima, E. O. Rapid prediction of solvation free energy. 1. An extensive test of linear interaction energy (LIE) J. Chem. Theory Comput. 2010, 6, 1608-1621
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1608-1621
-
-
Sulea, T.1
Corbeil, C.R.2
Purisima, E.O.3
-
16
-
-
77950650980
-
Towards accurate free energy calculations in ligand protein-binding studies
-
Steinbrecher, T.; Labahn, A. Towards accurate free energy calculations in ligand protein-binding studies Curr. Med. Chem. 2010, 17, 767-785
-
(2010)
Curr. Med. Chem.
, vol.17
, pp. 767-785
-
-
Steinbrecher, T.1
Labahn, A.2
-
17
-
-
79953075221
-
Alchemical free energy methods for drug discovery: Progress and challenges
-
Chodera, J. D.; Mobley, D. L.; Shirts, M. R.; Dixon, R. W.; Branson, K.; Pande, V. S. Alchemical free energy methods for drug discovery: Progress and challenges Curr. Opin. Struct. Biol. 2011, 21, 150-160
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 150-160
-
-
Chodera, J.D.1
Mobley, D.L.2
Shirts, M.R.3
Dixon, R.W.4
Branson, K.5
Pande, V.S.6
-
18
-
-
70349100806
-
Theory of free energy and entropy in noncovalent binding
-
Zhou, H.-X.; Gilson, M. K. Theory of free energy and entropy in noncovalent binding Chem. Rev. 2009, 109, 4092-4107
-
(2009)
Chem. Rev.
, vol.109
, pp. 4092-4107
-
-
Zhou, H.-X.1
Gilson, M.K.2
-
19
-
-
84865093289
-
-
Schrödinger, Inc. Portland, OR
-
OPLS2.0; Schrödinger, Inc.: Portland, OR, 2011.
-
(2011)
OPLS2.0
-
-
-
20
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations J. Mol. Graphics Modell. 2006, 25, 247-260
-
(2006)
J. Mol. Graphics Modell.
, vol.25
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
21
-
-
0001041959
-
Fast, efficient generation of high-quality atomic charges. Am1-bcc model: I. Method
-
Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. Fast, efficient generation of high-quality atomic charges. Am1-bcc model: I. Method J. Comput. Chem. 2000, 21, 132-146
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 132-146
-
-
Jakalian, A.1
Bush, B.L.2
Jack, D.B.3
Bayly, C.4
-
22
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. Am1-bcc model: II. Parameterization and validation
-
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
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
23
-
-
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
-
24
-
-
84986505827
-
Validation of the general-purpose Quanta 3.2/CHARMm force-field
-
Momany, F. A.; Rone, R. Validation of the general-purpose Quanta 3.2/CHARMm force-field J. Comput. Chem. 1992, 13, 888-900
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 888-900
-
-
Momany, F.A.1
Rone, R.2
-
25
-
-
0033606250
-
OPLS all-atom model for amines: Resolution of the amine hydration problem
-
Rizzo, R. C.; Jorgensen, W. L. OPLS all-atom model for amines: Resolution of the amine hydration problem J. Am. Chem. Soc. 1999, 121, 4827-4836
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 4827-4836
-
-
Rizzo, R.C.1
Jorgensen, W.L.2
-
26
-
-
0042296402
-
OPLS all-atom force field for carbohydrates
-
Damm, W.; Frontera, A.; Tirado-Rives, J.; Jorgensen, W. L. OPLS all-atom force field for carbohydrates J. Comput. Chem. 1997, 18, 1955-1970
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1955-1970
-
-
Damm, W.1
Frontera, A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
27
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 1996, 118, 11225-11236
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
28
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-aa force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski, G. A.; Friesner, R. A.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparametrization of the OPLS-aa force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105, 6474-6487
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
29
-
-
33846191634
-
Halide, ammonium, and alkali metal ion parameters for modeling aqueous solutions
-
Jensen, K. P.; Jorgensen, W. L. Halide, ammonium, and alkali metal ion parameters for modeling aqueous solutions J. Chem. Theory Comput. 2006, 2, 1499-1509
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1499-1509
-
-
Jensen, K.P.1
Jorgensen, W.L.2
-
30
-
-
0001061464
-
Merck molecular force field. IV. Conformational energies and geometries for MMFF94
-
Halgren, T. A.; Nachbar, R. B. Merck molecular force field. IV. Conformational energies and geometries for MMFF94 J. Comput. Chem. 1996, 17, 587-615
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 587-615
-
-
Halgren, T.A.1
Nachbar, R.B.2
-
31
-
-
25144517646
-
Integrated modeling program, applied chemical theory (IMPACT)
-
Banks, J. L.; Beard, H. S.; Cao, Y.; Cho, A. E.; Damm, W.; Farid, R.; Felts, A. K.; Halgren, T. A.; Mainz, D. T.; Maple, J. R.; Murphy, R.; Philipp, D. M.; Repasky, M. P.; Zhang, L. Y.; Berne, B. J.; Friesner, R. A.; Gallicchio, E.; Levy, R. M. Integrated modeling program, applied chemical theory (IMPACT) J. Comput. Chem. 2005, 26, 1752-1780
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1752-1780
-
-
Banks, J.L.1
Beard, H.S.2
Cao, Y.3
Cho, A.E.4
Damm, W.5
Farid, R.6
Felts, A.K.7
Halgren, T.A.8
Mainz, D.T.9
Maple, J.R.10
Murphy, R.11
Philipp, D.M.12
Repasky, M.P.13
Zhang, L.Y.14
Berne, B.J.15
Friesner, R.A.16
Gallicchio, E.17
Levy, R.M.18
-
32
-
-
0029248338
-
Class IV charge models: A new semiempirical approach in quantum chemistry
-
Storer, J. W.; Giesen, D. J.; Cramer, C. J.; Truhlar, D. G. Class IV charge models: A new semiempirical approach in quantum chemistry J. Comput.-Aided Mol. Des 2004, 9, 87-110
-
(2004)
J. Comput.-Aided Mol. des
, vol.9
, pp. 87-110
-
-
Storer, J.W.1
Giesen, D.J.2
Cramer, C.J.3
Truhlar, D.G.4
-
33
-
-
84865093964
-
-
v3.0; D. E. Shaw Research: New York
-
Desmond, v3.0; D. E. Shaw Research: New York, 2011.
-
(2011)
Desmond
-
-
-
35
-
-
40749131831
-
-
ACM: New York
-
Bowers, K. J.; Chow, E.; Xu, H.; Dror, R. O.; Eastwood, M. P.; Gregersen, B. A.; Klepeis, J. L.; Kolossvary, I.; Moraes, M. A.; Sacerdoti, F. D.; Salmon, J. K.; Shan, Y.; Shaw, D. E. In Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters; ACM: New York, 2006; p 84.
-
(2006)
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
, pp. 84
-
-
Bowers, K.J.1
Chow, E.2
Xu, H.3
Dror, R.O.4
Eastwood, M.P.5
Gregersen, B.A.6
Klepeis, J.L.7
Kolossvary, I.8
Moraes, M.A.9
Sacerdoti, F.D.10
Salmon, J.K.11
Shan, Y.12
Shaw, D.E.13
-
36
-
-
84865088282
-
-
v9.2; Schrödinger, Inc. Portland, OR
-
Maestro, v9.2; Schrödinger, Inc.: Portland, OR, 2011.
-
(2011)
Maestro
-
-
-
37
-
-
5244304444
-
Efficient estimation of free energy differences from Monte Carlo data
-
Bennett, C. H. Efficient estimation of free energy differences from Monte Carlo data J. Comput. Phys. 1976, 22, 245-268
-
(1976)
J. Comput. Phys.
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
|