-
1
-
-
18744387415
-
Potential Energy Functions for Atomic-Level Simulations of Water and Organic and Biomolecular Systems
-
Jorgensen, W. L.; Tirado-Rives, J. Potential Energy Functions for Atomic-Level Simulations of Water and Organic and Biomolecular Systems Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6665 - 6670
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 6665-6670
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
2
-
-
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
-
3
-
-
84855671158
-
Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Compressibility, Expansion Coefficient and Dielectric Constant
-
Caleman, C.; van Maaren, P. J.; Hong, M.; Hub, J. S.; Costa, L. T.; van der Spoel, D. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Compressibility, Expansion Coefficient and Dielectric Constant J. Chem. Theory Comput. 2012, 8, 61 - 74
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 61-74
-
-
Caleman, C.1
Van Maaren, P.J.2
Hong, M.3
Hub, J.S.4
Costa, L.T.5
Van Der Spoel, D.6
-
4
-
-
0141990949
-
Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins
-
Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins J. Chem. Phys. 2003, 119, 5740 - 5761
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 5740-5761
-
-
Shirts, M.R.1
Pitera, J.W.2
Swope, W.C.3
Pande, V.S.4
-
5
-
-
33748791718
-
Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models
-
Hess, B.; van der Vegt, N. F. A. Hydration Thermodynamic Properties of Amino Acid Analogues: A Systematic Comparison of Biomolecular Force Fields and Water Models J. Phys. Chem. B 2006, 110, 17616 - 17626
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 17616-17626
-
-
Hess, B.1
Van Der Vegt, N.F.A.2
-
6
-
-
65249112693
-
Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations
-
Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Dill, K. A. Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113, 4533 - 4537
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 4533-4537
-
-
Mobley, D.L.1
Bayly, C.I.2
Cooper, M.D.3
Dill, K.A.4
-
7
-
-
65249187748
-
Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations
-
Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations J. Chem. Theory Comput. 2009, 5, 350 - 358
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 350-358
-
-
Mobley, D.L.1
Bayly, C.I.2
Cooper, M.D.3
Shirts, M.R.4
Dill, K.A.5
-
8
-
-
84924405768
-
Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations
-
Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations J. Chem. Theory Comput. 2015, 11, 1347 - 1347
-
(2015)
J. Chem. Theory Comput.
, vol.11
, pp. 1347-1347
-
-
Mobley, D.L.1
Bayly, C.I.2
Cooper, M.D.3
Shirts, M.R.4
Dill, K.A.5
-
9
-
-
4444282928
-
A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6
-
Oostenbrink, C.; Villa, A.; Mark, A. E.; Van Gunsteren, W. F. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation: The GROMOS Force-Field Parameter Sets 53A5 and 53A6 J. Comput. Chem. 2004, 25, 1656 - 1676
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
Van Gunsteren, W.F.4
-
10
-
-
84904130280
-
Practical Aspects of Free-Energy Calculations: A Review
-
Hansen, N.; van Gunsteren, W. F. Practical Aspects of Free-Energy Calculations: A Review J. Chem. Theory Comput. 2014, 10, 2632 - 2647
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 2632-2647
-
-
Hansen, N.1
Van Gunsteren, W.F.2
-
11
-
-
31944434856
-
Combination of a Modified Scoring Function with Two-Dimensional Descriptors for Calculation of Binding Affinities of Bulky, Flexible Ligands to Proteins
-
Hetenyi, C.; Paragi, G.; Maran, U.; Timar, Z.; Karelson, M.; Penke, B. Combination of a Modified Scoring Function with Two-Dimensional Descriptors for Calculation of Binding Affinities of Bulky, Flexible Ligands to Proteins J. Am. Chem. Soc. 2006, 128, 1233 - 1239
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 1233-1239
-
-
Hetenyi, C.1
Paragi, G.2
Maran, U.3
Timar, Z.4
Karelson, M.5
Penke, B.6
-
12
-
-
79951535155
-
Statistical Approaches to Forcefield Calibration and Prediction Uncertainty in Molecular Simulation
-
Cailliez, F.; Pernot, P. Statistical Approaches to Forcefield Calibration and Prediction Uncertainty in Molecular Simulation J. Chem. Phys. 2011, 134, 054124
-
(2011)
J. Chem. Phys.
, vol.134
-
-
Cailliez, F.1
Pernot, P.2
-
13
-
-
77749298172
-
Current Status of the AMOEBA Polarizable Force Field
-
Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A., Jr.; Head-Gordon, M.; Clark, G. N. I.; Johnson, M. E.; Head-Gordon, T. Current Status of the AMOEBA Polarizable Force Field J. Phys. Chem. B 2010, 114, 2549 - 2564
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 2549-2564
-
-
Ponder, J.W.1
Wu, C.2
Ren, P.3
Pande, V.S.4
Chodera, J.D.5
Schnieders, M.J.6
Haque, I.7
Mobley, D.L.8
Lambrecht, D.S.9
DiStasio, R.A.10
Head-Gordon, M.11
Clark, G.N.I.12
Johnson, M.E.13
Head-Gordon, T.14
-
14
-
-
84890447773
-
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
-
Lopes, P. E. M.; Huang, J.; Shim, J.; Luo, Y.; Li, H.; Roux, B.; MacKerell, J.; Alexander, D. Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator J. Chem. Theory Comput 2013, 9, 5430 - 5449
-
(2013)
J. Chem. Theory Comput
, vol.9
, pp. 5430-5449
-
-
Lopes, P.E.M.1
Huang, J.2
Shim, J.3
Luo, Y.4
Li, H.5
Roux, B.6
MacKerell, J.7
Alexander, D.8
-
15
-
-
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
-
16
-
-
79952833958
-
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 2011, 115, 1329 - 1332
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 1329-1332
-
-
Mobley, D.L.1
Dumont, E.2
Chodera, J.D.3
Dill, K.A.4
-
17
-
-
84906272546
-
Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field
-
Martins, S. A.; Sousa, S. F.; Ramos, M. J.; Fernandes, P. A. Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field J. Chem. Theory Comput. 2014, 10, 3570 - 3577
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 3570-3577
-
-
Martins, S.A.1
Sousa, S.F.2
Ramos, M.J.3
Fernandes, P.A.4
-
18
-
-
84875365986
-
Assessing the Uality of Absolute Hydration Free Energies among CHARMM-Compatible Ligand Parameterization Schemes
-
Knight, J. L.; Yesselman, J. D.; Brooks, C. L. Assessing the Uality of Absolute Hydration Free Energies Among CHARMM-Compatible Ligand Parameterization Schemes J. Comput. Chem. 2013, 34, 893 - 903
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 893-903
-
-
Knight, J.L.1
Yesselman, J.D.2
Brooks, C.L.3
-
19
-
-
0000795938
-
Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model
-
Kaminski, G.; Duffy, E. M.; Matsui, T.; Jorgensen, W. L. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model J. Phys. Chem. 1994, 98, 13077 - 13082
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 13077-13082
-
-
Kaminski, G.1
Duffy, E.M.2
Matsui, T.3
Jorgensen, W.L.4
-
20
-
-
3142707941
-
Accuracy of Free Energies of Hydration Using CM1 and CM3 Atomic Charges
-
Udier-Blagovic, M.; Tirado, P. M. D.; 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
Tirado, P.M.D.2
Pearlman, S.A.3
Jorgensen, W.L.4
-
21
-
-
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
-
22
-
-
84865069436
-
Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field
-
Shivakumar, D.; Harder, E.; Damm, W.; Friesner, R. A.; Sherman, W. Improving the Prediction of Absolute Solvation Free Energies Using the Next Generation OPLS Force Field J. Chem. Theory Comput. 2012, 8, 2553 - 2558
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2553-2558
-
-
Shivakumar, D.1
Harder, E.2
Damm, W.3
Friesner, R.A.4
Sherman, W.5
-
23
-
-
84962420681
-
Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method
-
Wallin, G.; Nervall, M.; Carlsson, J.; Åqvist, J. Charges for Large Scale Binding Free Energy Calculations with the Linear Interaction Energy Method J. Chem. Theory Comput. 2009, 5, 380 - 395
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 380-395
-
-
Wallin, G.1
Nervall, M.2
Carlsson, J.3
Åqvist, J.4
-
24
-
-
79954480884
-
New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters
-
Horta, B. A. C.; Fuchs, P. F. J.; van Gunsteren, W. F.; Hunenberger, P. H. New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters J. Chem. Theory Comput. 2011, 7, 1016 - 1031
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1016-1031
-
-
Horta, B.A.C.1
Fuchs, P.F.J.2
Van Gunsteren, W.F.3
Hunenberger, P.H.4
-
25
-
-
84867350009
-
A GROMOS Parameter Set for Vicinal Diether Functions: Properties of Polyethyleneoxide and Polyethyleneglycol
-
Fuchs, P. F. J.; Hansen, H. S.; Hünenberger, P. H.; Horta, B. A. C. A GROMOS Parameter Set for Vicinal Diether Functions: Properties of Polyethyleneoxide and Polyethyleneglycol J. Chem. Theory Comput. 2012, 8, 3943 - 3963
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3943-3963
-
-
Fuchs, P.F.J.1
Hansen, H.S.2
Hünenberger, P.H.3
Horta, B.A.C.4
-
26
-
-
0030256107
-
Molecular Dynamics Simulations of Peptides from BPTI: A Closer Look at Amide-Aromatic Interactions
-
van der Spoel, D.; van Buuren, A. R.; Tieleman, D. P.; Berendsen, H. J. C. Molecular Dynamics Simulations of Peptides from BPTI: A Closer Look at Amide-Aromatic Interactions J. Biomol. NMR 1996, 8, 229 - 238
-
(1996)
J. Biomol. NMR
, vol.8
, pp. 229-238
-
-
Van Der Spoel, D.1
Van Buuren, A.R.2
Tieleman, D.P.3
Berendsen, H.J.C.4
-
27
-
-
0242292035
-
Brute-Force Molecular Dynamics Simulations of Villin Headpiece: Comparison with NMR Parameters
-
van der Spoel, D.; Lindahl, E. Brute-Force Molecular Dynamics Simulations of Villin Headpiece: Comparison with NMR Parameters J. Phys. Chem. B 2003, 107, 11178 - 11187
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 11178-11187
-
-
Van Der Spoel, D.1
Lindahl, E.2
-
28
-
-
0344178265
-
A general Treatment of Solubility. 1. The QSPR Correlation of Solvation Free Energies of Single Solutes in Series of Solvents
-
Katritzky, A. R.; Oliferenko, A. A.; Oliferenko, P. V.; Petrukhin, R.; Tatham, D. B.; Maran, U.; Lomaka, A.; Acree, W. E. A general Treatment of Solubility. 1. The QSPR Correlation of Solvation Free Energies of Single Solutes in Series of Solvents J. Chem. Inf. Comput. Sci. 2003, 43, 1794 - 1805
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 1794-1805
-
-
Katritzky, A.R.1
Oliferenko, A.A.2
Oliferenko, P.V.3
Petrukhin, R.4
Tatham, D.B.5
Maran, U.6
Lomaka, A.7
Acree, W.E.8
-
29
-
-
0344686537
-
A General Treatment of Solubility. 2. QSPR Prediction of Free Energies of Solvation of Specified Solutes in Ranges of Solvents
-
Katritzky, A. R.; Oliferenko, A. A.; Oliferenko, P. V.; Petrukhin, R.; Tatham, D. B.; Maran, U.; Lomaka, A.; Acree, W. E. A General Treatment of Solubility. 2. QSPR Prediction of Free Energies of Solvation of Specified Solutes in Ranges of Solvents J. Chem. Inf. Comput. Sci. 2003, 43, 1806 - 1814
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 1806-1814
-
-
Katritzky, A.R.1
Oliferenko, A.A.2
Oliferenko, P.V.3
Petrukhin, R.4
Tatham, D.B.5
Maran, U.6
Lomaka, A.7
Acree, W.E.8
-
30
-
-
23844495579
-
A General Treatment of Solubility. 3. Principal Component Analysis (PCA) of the Solubilities of Diverse Solutes in Diverse Solvents
-
Katritzky, A. R.; Tulp, I.; Fara, D. C.; Lauria, A.; Maran, U.; Acree, W. E. A General Treatment of Solubility. 3. Principal Component Analysis (PCA) of the Solubilities of Diverse Solutes in Diverse Solvents J. Chem. Inf. Model. 2005, 45, 913 - 923
-
(2005)
J. Chem. Inf. Model.
, vol.45
, pp. 913-923
-
-
Katritzky, A.R.1
Tulp, I.2
Fara, D.C.3
Lauria, A.4
Maran, U.5
Acree, W.E.6
-
31
-
-
33751157086
-
Conductor-like Screening Model for Real Solvents: A New Approach to the Quantitative Calculation of Solvation Phenomena
-
Klamt, A. Conductor-like Screening Model for Real Solvents: A New Approach to the Quantitative Calculation of Solvation Phenomena J. Phys. Chem. 1995, 99, 2224 - 2235
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 2224-2235
-
-
Klamt, A.1
-
32
-
-
4244072997
-
Refinement and Parametrization of COSMO-RS
-
Klamt, A.; Jonas, V.; Bürger, T.; Lohrenz, J. C. W. Refinement and Parametrization of COSMO-RS J. Phys. Chem. A 1998, 102, 5074 - 5085
-
(1998)
J. Phys. Chem. A
, vol.102
, pp. 5074-5085
-
-
Klamt, A.1
Jonas, V.2
Bürger, T.3
Lohrenz, J.C.W.4
-
33
-
-
0021372124
-
The Ostwald coefficient of gas solubility
-
Battino, R. The Ostwald coefficient of gas solubility Fluid Phase Equilib. 1984, 15, 231 - 240
-
(1984)
Fluid Phase Equilib.
, vol.15
, pp. 231-240
-
-
Battino, R.1
-
34
-
-
0000249851
-
Avoiding Singularities and Numerical Instabilities in Free Energy Calculations Based on Molecular Simulations
-
Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F. Avoiding Singularities and Numerical Instabilities in Free Energy Calculations Based on Molecular Simulations Chem. Phys. Lett. 1994, 222, 529 - 539
-
(1994)
Chem. Phys. Lett.
, vol.222
, pp. 529-539
-
-
Beutler, T.C.1
Mark, A.E.2
Van Schaik, R.C.3
Gerber, P.R.4
Van Gunsteren, W.F.5
-
35
-
-
23944432199
-
Comparison of Efficiency and Bias of Free Energies Computed by Exponential Averaging, the Bennett Acceptance Ratio, and Thermodynamic Integration
-
Shirts, M. R.; Pande, V. S. Comparison of Efficiency and Bias of Free Energies Computed by Exponential Averaging, the Bennett Acceptance Ratio, and Thermodynamic Integration J. Chem. Phys. 2005, 122, 144107
-
(2005)
J. Chem. Phys.
, vol.122
-
-
Shirts, M.R.1
Pande, V.S.2
-
36
-
-
0029633168
-
GROMACS: A message-passing parallel molecular dynamics implementation
-
Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation Comput. Phys. Commun. 1995, 91, 43 - 56
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
Van Der Spoel, D.2
Van Drunen, R.3
-
37
-
-
0035789518
-
GROMACS 3.0: A Package for Molecular Simulation and Trajectory Analysis
-
Lindahl, E.; Hess, B.; Van Der Spoel, D. GROMACS 3.0: a Package for Molecular Simulation and Trajectory Analysis J. Mol. Model 2001, 7, 306 - 317
-
(2001)
J. Mol. Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
38
-
-
27344454932
-
GROMACS: Fast, Flexible and Free
-
van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, Flexible and Free J. Comput. Chem. 2005, 26, 1701 - 1718
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.C.6
-
39
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; Van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435 - 447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
40
-
-
84875592758
-
GROMACS 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit
-
Pronk, S.; Páll, S.; Schulz, R.; Larsson, P.; Bjelkmar, P.; Apostolov, R.; Shirts, M. R.; Smith, J. C.; Kasson, P. M.; van der Spoel, D.; Hess, B.; Lindahl, E. GROMACS 4.5: a High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit Bioinformatics 2013, 29, 845 - 854
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk, S.1
Páll, S.2
Schulz, R.3
Larsson, P.4
Bjelkmar, P.5
Apostolov, R.6
Shirts, M.R.7
Smith, J.C.8
Kasson, P.M.9
Van Der Spoel, D.10
Hess, B.11
Lindahl, E.12
-
41
-
-
84857872128
-
GROMACS Molecule & Liquid Database
-
van der Spoel, D.; van Maaren, P. J.; Caleman, C. GROMACS Molecule & Liquid Database Bioinformatics 2012, 28, 752 - 753
-
(2012)
Bioinformatics
, vol.28
, pp. 752-753
-
-
Van Der Spoel, D.1
Van Maaren, P.J.2
Caleman, C.3
-
42
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, 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
Impey, R.W.4
Klein, M.L.5
-
43
-
-
7544226311
-
PRODRG - A Tool for High-Throughput Crystallography of Protein-Ligand Complexes
-
Schuettelkopf, A. W.; van Aalten, D. M. F. PRODRG-a Tool for High-Throughput Crystallography of Protein-Ligand Complexes Act. Crystallogr. D 2004, 60, 1355 - 1363
-
(2004)
Act. Crystallogr. D
, vol.60
, pp. 1355-1363
-
-
Schuettelkopf, A.W.1
Van Aalten, D.M.F.2
-
44
-
-
0033963034
-
Molden: A Pre- and Post-Processing Program for Molecular and Electronic Structures
-
Schaftenaar, G.; Noordik, J. H. Molden: a Pre- and Post-Processing Program for Molecular and Electronic Structures J. Comput. Aid. Mol. Des. 2000, 14, 123 - 134
-
(2000)
J. Comput. Aid. Mol. Des.
, vol.14
, pp. 123-134
-
-
Schaftenaar, G.1
Noordik, J.H.2
-
46
-
-
26844534384
-
Self-consistent Molecular-orbital Methods. 20. Basis Set for Correlated Wave-functions
-
Krishnan, R.; Binkley, J. S.; Seeger, R.; Pople, J. A. Self-consistent Molecular-orbital Methods. 20. Basis Set for Correlated Wave-functions J. Chem. Phys. 1980, 72, 650 - 654
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 650-654
-
-
Krishnan, R.1
Binkley, J.S.2
Seeger, R.3
Pople, J.A.4
-
47
-
-
0141509423
-
Contracted Gaussian-basis Sets for Molecular Calculations. 1. 2nd Row Atoms, Z=11-18
-
McLean, A. D.; Chandler, G. S. Contracted Gaussian-basis Sets for Molecular Calculations. 1. 2nd Row Atoms, Z=11-18 J. Chem. Phys. 1980, 72, 5639 - 5648
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 5639-5648
-
-
McLean, A.D.1
Chandler, G.S.2
-
48
-
-
33645200462
-
Antechamber, an Accessory Software Package for Molecular Mechanical Calculations
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Antechamber, an Accessory Software Package for Molecular Mechanical Calculations J. Comput. Chem. 2005, 25, 1157 - 1174
-
(2005)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
49
-
-
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
-
50
-
-
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, 84902
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 84902
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
-
51
-
-
84943200457
-
A Leap-Frog Algorithm for Stochastic Dynamics
-
van Gunsteren, W. F.; Berendsen, H. J. C. A Leap-Frog Algorithm for Stochastic Dynamics Mol. Sim. 1988, 1, 173 - 185
-
(1988)
Mol. Sim.
, vol.1
, pp. 173-185
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
52
-
-
0000388705
-
LINCS: A Linear Constraint Solver for Molecular Simulations
-
Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463 - 1472
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
53
-
-
38749123962
-
P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
-
Hess, B. P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation J. Chem. Theory Comput. 2008, 4, 116 - 122
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 116-122
-
-
Hess, B.1
-
54
-
-
0019707626
-
Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method
-
Parrinello, M.; Rahman, A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method J. Appl. Phys. 1981, 52, 7182 - 7190
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7190
-
-
Parrinello, M.1
Rahman, A.2
-
56
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577 - 8592
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8592
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
57
-
-
68349094070
-
An Implementation of the Conductor-Like Screening Model of Solvation within the Amsterdam Density Functional Package - Part II. COSMO for Real Solvents 1
-
Pye, C. C.; Ziegler, T.; van Lenthe, E.; Louwen, J. N. An Implementation of the Conductor-Like Screening Model of Solvation within the Amsterdam Density Functional Package-Part II. COSMO for Real Solvents 1 Can. J. Chem. 2009, 87, 790 - 797
-
(2009)
Can. J. Chem.
, vol.87
, pp. 790-797
-
-
Pye, C.C.1
Ziegler, T.2
Van Lenthe, E.3
Louwen, J.N.4
-
58
-
-
33745629602
-
Sigma-Profile Database for Using COSMO-Based Thermodynamic Methods
-
Mullins, E.; Oldland, R.; Liu, Y. A.; Wang, S.; Sandler, S. I.; Chen, C.-C.; Zwolak, M.; Seavey, K. C. Sigma-Profile Database for Using COSMO-Based Thermodynamic Methods Ind. Eng. Chem. Res. 2006, 45, 4389 - 4415
-
(2006)
Ind. Eng. Chem. Res.
, vol.45
, pp. 4389-4415
-
-
Mullins, E.1
Oldland, R.2
Liu, Y.A.3
Wang, S.4
Sandler, S.I.5
Chen, C.-C.6
Zwolak, M.7
Seavey, K.C.8
-
59
-
-
41749098616
-
Sigma Profile Database for Predicting Solid Solubility in Pure and Mixed Solvent Mixtures for Organic Pharmacological Compounds with COSMO-Based Thermodynamic Methods
-
Mullins, E.; Liu, Y. A.; Ghaderi, A.; Fast, S. D. Sigma Profile Database for Predicting Solid Solubility in Pure and Mixed Solvent Mixtures for Organic Pharmacological Compounds with COSMO-Based Thermodynamic Methods Ind. Eng. Chem. Res. 2008, 47, 1707 - 1725
-
(2008)
Ind. Eng. Chem. Res.
, vol.47
, pp. 1707-1725
-
-
Mullins, E.1
Liu, Y.A.2
Ghaderi, A.3
Fast, S.D.4
-
60
-
-
56449095230
-
Quantum Mechanical Predictions of the Henry's Law Constants and Their Temperature Dependence for the 209 Polychlorinated Biphenyl Congeners
-
Phillips, K. L.; Sandler, S. I.; Greene, R. W.; Toro, D. M. D. Quantum Mechanical Predictions of the Henry's Law Constants and Their Temperature Dependence for the 209 Polychlorinated Biphenyl Congeners Environ. Sci. Technol. 2008, 42, 8412 - 8418
-
(2008)
Environ. Sci. Technol.
, vol.42
, pp. 8412-8418
-
-
Phillips, K.L.1
Sandler, S.I.2
Greene, R.W.3
Toro, D.M.D.4
-
61
-
-
34247272948
-
Evaluating Virtual Screening Methods: Good and Bad Metrics for the "Early Recognition" Problem
-
Truchon, J.-F.; Bayly, C. I. Evaluating Virtual Screening Methods: Good and Bad Metrics for the "Early Recognition" Problem J. Chem. Inf. Model. 2007, 47, 488 - 508
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 488-508
-
-
Truchon, J.-F.1
Bayly, C.I.2
-
62
-
-
77952832818
-
A CROC Stronger than ROC: Measuring, Visualizing and Optimizing Early Retrieval
-
Swamidass, S. J.; Azencott, C.-A.; Daily, K.; Baldi, P. A CROC Stronger than ROC: Measuring, Visualizing and Optimizing Early Retrieval Bioinformatics 2010, 26, 1348 - 1356
-
(2010)
Bioinformatics
, vol.26
, pp. 1348-1356
-
-
Swamidass, S.J.1
Azencott, C.-A.2
Daily, K.3
Baldi, P.4
-
63
-
-
77956123443
-
Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: An Open-Source Approach
-
Haider, N. Functionality Pattern Matching as an Efficient Complementary Structure/Reaction Search Tool: an Open-Source Approach Molecules 2010, 15, 5079 - 5092
-
(2010)
Molecules
, vol.15
, pp. 5079-5092
-
-
Haider, N.1
-
65
-
-
0033269427
-
Extension of the Platform of Applicability of the SM5.42R Universal Solvation Model
-
Li, J.; Zhu, T.; Hawkins, G. D.; Winget, P.; Liotard, D. A.; Cramer, C. J.; Truhlar, D. G. Extension of the Platform of Applicability of the SM5.42R Universal Solvation Model Theor. Chem. Acc. 1999, 103, 9 - 63
-
(1999)
Theor. Chem. Acc.
, vol.103
, pp. 9-63
-
-
Li, J.1
Zhu, T.2
Hawkins, G.D.3
Winget, P.4
Liotard, D.A.5
Cramer, C.J.6
Truhlar, D.G.7
-
66
-
-
79955556311
-
Atomistic Simulation of Ion Solvation in Water Explains Surface Preference of Halides
-
Caleman, C.; Hub, J. S.; van Maaren, P. J.; van der Spoel, D. Atomistic Simulation of Ion Solvation in Water Explains Surface Preference of Halides Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 6838 - 6842
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 6838-6842
-
-
Caleman, C.1
Hub, J.S.2
Van Maaren, P.J.3
Van Der Spoel, D.4
-
67
-
-
84862858652
-
Organic Molecules on the Surface of Water Droplets an Energetic Perspective
-
Hub, J. S.; Caleman, C.; van der Spoel, D. Organic Molecules on the Surface of Water Droplets an Energetic Perspective Phys. Chem. Chem. Phys. 2012, 14, 9537 - 9545
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 9537-9545
-
-
Hub, J.S.1
Caleman, C.2
Van Der Spoel, D.3
-
68
-
-
84898064511
-
Thermodynamics of Hydronium and Hydroxide Surface Solvation
-
Hub, J. S.; Wolf, M. G.; Caleman, C.; van Maaren, P. J.; Groenhof, G.; van der Spoel, D. Thermodynamics of Hydronium and Hydroxide Surface Solvation Chem. Sci. 2014, 5, 1745 - 1749
-
(2014)
Chem. Sci.
, vol.5
, pp. 1745-1749
-
-
Hub, J.S.1
Wolf, M.G.2
Caleman, C.3
Van Maaren, P.J.4
Groenhof, G.5
Van Der Spoel, D.6
-
69
-
-
84879126441
-
Hydration Free Energies of Multifunctional Nitroaromatic Compounds
-
Ahmed, A.; Sandler, S. I. Hydration Free Energies of Multifunctional Nitroaromatic Compounds J. Chem. Theory Comput. 2013, 9, 2774 - 2785
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 2774-2785
-
-
Ahmed, A.1
Sandler, S.I.2
-
70
-
-
84986468608
-
An Approach to Computing Electrostatic Charges for Molecules
-
Singh, U. C.; Kollman, P. A. An Approach to Computing Electrostatic Charges for Molecules J. Comput. Chem. 1984, 5, 129 - 145
-
(1984)
J. Comput. Chem.
, vol.5
, pp. 129-145
-
-
Singh, U.C.1
Kollman, P.A.2
-
71
-
-
84986492477
-
Atomic Charges Derived from Semiempirical Methods
-
Besler, B. H.; Merz, K. M., Jr.; 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
-
72
-
-
0343380162
-
Charges Fit to Electrostatic Potentials. 2. Can Atomic Charges be Unambiguously Fit to Electrostatic Potentials?
-
Francl, M. M.; Carey, C.; Chirlian, L. E.; Gange, D. M. Charges Fit to Electrostatic Potentials. 2. Can Atomic Charges be Unambiguously Fit to Electrostatic Potentials? J. Comput. Chem. 1996, 17, 367 - 383
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 367-383
-
-
Francl, M.M.1
Carey, C.2
Chirlian, L.E.3
Gange, D.M.4
-
73
-
-
0034424016
-
The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials
-
Francl, M. M.; Chirlian, L. E. The Pluses and Minuses of Mapping Atomic Charges to Electrostatic Potentials Rev. Comput. Chem. 2000, 14, 1 - 31
-
(2000)
Rev. Comput. Chem.
, vol.14
, pp. 1-31
-
-
Francl, M.M.1
Chirlian, L.E.2
-
74
-
-
11644300961
-
Comparison of Methods for Deriving Atomic Charges from the Electrostatic Potential and Moments
-
Sigfridsson, E.; Ryde, U. Comparison of Methods for Deriving Atomic Charges from the Electrostatic Potential and Moments J. Comput. Chem. 1998, 19, 377 - 395
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 377-395
-
-
Sigfridsson, E.1
Ryde, U.2
-
75
-
-
79960216924
-
Application of Molecular Dynamics Simulations in Molecular Property Prediction. 1. Density and Heat of Vaporization
-
Wang, J.; Tingjun, H. Application of Molecular Dynamics Simulations in Molecular Property Prediction. 1. Density and Heat of Vaporization J. Chem. Theory Comput. 2011, 7, 2151 - 2165
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 2151-2165
-
-
Wang, J.1
Tingjun, H.2
-
76
-
-
0034728673
-
Prediction of Properties from Simulations: Free Energies of Solvation in Hexadecane, Octanol, and Water
-
Duffy, E.; Jorgensen, W. Prediction of Properties from Simulations: Free Energies of Solvation in Hexadecane, Octanol, and Water J. Am. Chem. Soc. 2000, 122, 2878 - 2888
-
(2000)
J. Am. Chem. Soc.
, vol.122
, pp. 2878-2888
-
-
Duffy, E.1
Jorgensen, W.2
-
77
-
-
23444454552
-
The Amber Biomolecular Simulation Programs
-
Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber Biomolecular Simulation Programs J. Comput. Chem. 2005, 26, 1668 - 1688
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz, K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
78
-
-
84921510376
-
Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations
-
Lundborg, M.; Lindahl, E. Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations J. Phys. Chem. B 2015, 119, 810 - 823
-
(2015)
J. Phys. Chem. B
, vol.119
, pp. 810-823
-
-
Lundborg, M.1
Lindahl, E.2
-
79
-
-
0030180875
-
New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects
-
Marten, B.; Kim, K.; Cortis, C.; Friesner, R. A.; Murphy, R. B.; Ringnalda, M. N.; Sitkoff, D.; Honig, B. New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects J. Phys. Chem. 1996, 100, 11775 - 11788
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 11775-11788
-
-
Marten, B.1
Kim, K.2
Cortis, C.3
Friesner, R.A.4
Murphy, R.B.5
Ringnalda, M.N.6
Sitkoff, D.7
Honig, B.8
-
80
-
-
84864647012
-
Reoptimized Interaction Parameters for the Peptide-Backbone Model Compound N-methylacetamide in the GROMOS Force Field: Influence on the Folding Properties of Two Beta-Peptides in Methanol
-
Horta, B. A. C.; Lin, Z.; Huang, W.; Riniker, S.; van Gunsteren, W. F.; Hünenberger, P. H. Reoptimized Interaction Parameters for the Peptide-Backbone Model Compound N-methylacetamide in the GROMOS Force Field: Influence on the Folding Properties of Two Beta-Peptides in Methanol J. Comput. Chem. 2012, 33, 1907 - 1917
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 1907-1917
-
-
Horta, B.A.C.1
Lin, Z.2
Huang, W.3
Riniker, S.4
Van Gunsteren, W.F.5
Hünenberger, P.H.6
-
81
-
-
34548524218
-
Fast evaluation of polarizable forces
-
Wang, W.; Skeel, R. D. Fast evaluation of polarizable forces J. Chem. Phys. 2005, 123, 164107
-
(2005)
J. Chem. Phys.
, vol.123
-
-
Wang, W.1
Skeel, R.D.2
-
82
-
-
25844474073
-
Accounting for polarization in molecular simulation
-
Yu, H. B.; van Gunsteren, W. F. Accounting for polarization in molecular simulation Comput. Phys. Commun. 2005, 172, 69 - 85
-
(2005)
Comput. Phys. Commun.
, vol.172
, pp. 69-85
-
-
Yu, H.B.1
Van Gunsteren, W.F.2
-
83
-
-
0142180089
-
Dynamic Properties of Water/Alcohol Mixtures Studied by Computer Simulation
-
Wensink, E. J. W.; Hoffmann, A. C.; van Maaren, P. J.; van der Spoel, D. Dynamic Properties of Water/Alcohol Mixtures Studied by Computer Simulation J. Chem. Phys. 2003, 119, 7308 - 7317
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 7308-7317
-
-
Wensink, E.J.W.1
Hoffmann, A.C.2
Van Maaren, P.J.3
Van Der Spoel, D.4
-
84
-
-
0001010885
-
The representation of van der Waals (vdW) interactions in molecular mechanics force fields: Potential form, combination rules, and vdW parameters
-
Halgren, T. A. The representation of van der Waals (vdW) interactions in molecular mechanics force fields: potential form, combination rules, and vdW parameters J. Am. Chem. Soc. 1992, 114, 7827 - 7843
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 7827-7843
-
-
Halgren, T.A.1
|