-
1
-
-
84862612207
-
Modeling Nucleic Acids
-
Sim, A. Y. L.; Minary, P.; Levitt, M. Modeling Nucleic Acids Curr. Opin. Struct. Biol. 2012, 22, 273-278
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 273-278
-
-
Sim, A.Y.L.1
Minary, P.2
Levitt, M.3
-
2
-
-
79953742584
-
Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems
-
Kamerlin, S. C. L.; Vicatos, S.; Dryga, A.; Warshel, A. Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems Annu. Rev. Phys. Chem. 2011, 62, 41-64
-
(2011)
Annu. Rev. Phys. Chem.
, vol.62
, pp. 41-64
-
-
Kamerlin, S.C.L.1
Vicatos, S.2
Dryga, A.3
Warshel, A.4
-
3
-
-
0036725277
-
Molecular Dynamics Simulations of Biomolecules
-
Karplus, M.; McCammon, J. A. Molecular Dynamics Simulations of Biomolecules Nat. Struct. Biol. 2002, 9, 646-652
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
4
-
-
84890447773
-
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator
-
Lopes, P. E.; Huang, J.; Shim, J.; Luo, Y.; Li, H.; Roux, B.; MacKerell, A. 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.1
Huang, J.2
Shim, J.3
Luo, Y.4
Li, H.5
Roux, B.6
Mackerell, A.D.7
-
5
-
-
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. 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, C.L.3
-
6
-
-
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. A. All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins J. Phys. Chem. B 1998, 102, 3586-3616
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.A.10
-
7
-
-
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
-
8
-
-
33645716062
-
Strike a Balance: Optimization of Backbone Torsion Parameters of AMBER Polarizable Force Field for Simulations of Proteins and Peptides
-
Wang, Z.-X.; Zhang, W.; Wu, C.; Lei, H.; Cieplak, P.; Duan, Y. Strike a Balance: Optimization of Backbone Torsion Parameters of AMBER Polarizable Force Field for Simulations of Proteins and Peptides J. Comput. Chem. 2006, 27, 781-790
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 781-790
-
-
Wang, Z.-X.1
Zhang, W.2
Wu, C.3
Lei, H.4
Cieplak, P.5
Duan, Y.6
-
9
-
-
84907992125
-
Ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins
-
Cerutti, D. S.; Swope, W. C.; Rice, J. E.; Case, D. A. Ff14ipq: A Self-Consistent Force Field for Condensed-Phase Simulations of Proteins J. Chem. Theory Comput. 2014, 10, 4515-4534
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 4515-4534
-
-
Cerutti, D.S.1
Swope, W.C.2
Rice, J.E.3
Case, D.A.4
-
10
-
-
21244467488
-
Validation of the 53A6 GROMOS Force Field
-
Oostenbrink, C.; Soares, T. A.; van der Vegt, N. F. A.; van Gunsteren, W. F. Validation of the 53A6 GROMOS Force Field Eur. Biophys. J. 2005, 34, 273-284
-
(2005)
Eur. Biophys. J.
, vol.34
, pp. 273-284
-
-
Oostenbrink, C.1
Soares, T.A.2
Van Der Vegt, N.F.A.3
Van Gunsteren, W.F.4
-
11
-
-
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
-
12
-
-
33645941402
-
The OPLS [optimized Potentials for Liquid Simulations] Potential Functions for Proteins, Energy Minimizations for Crystals of Cyclic Peptides and Crambin
-
Jorgensen, W. L.; Tirado-Rives, J. The OPLS [optimized Potentials for Liquid Simulations] Potential Functions for Proteins, Energy Minimizations for Crystals of Cyclic Peptides and Crambin J. Am. Chem. Soc. 1988, 110, 1657-1666
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
13
-
-
84890495015
-
Forcefield-PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-translational Modifications
-
Khoury, G. A.; Thompson, J. P.; Smadbeck, J.; Kieslich, C. A.; Floudas, C. A. Forcefield-PTM: Ab Initio Charge and AMBER Forcefield Parameters for Frequently Occurring Post-translational Modifications J. Chem. Theory Comput. 2013, 9, 5653-5674
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 5653-5674
-
-
Khoury, G.A.1
Thompson, J.P.2
Smadbeck, J.3
Kieslich, C.A.4
Floudas, C.A.5
-
14
-
-
84864045276
-
Development of Polarizable Models for Molecular Mechanical Calculations. 3. Polarizable Water Models Conforming to Thole Polarization Screening Schemes
-
Wang, J.; Cieplak, P.; Cai, Q.; Hsieh, M.-J.; Wang, J.; Duan, Y.; Luo, R. Development of Polarizable Models for Molecular Mechanical Calculations. 3. Polarizable Water Models Conforming to Thole Polarization Screening Schemes J. Phys. Chem. B 2012, 116, 7999-8008
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 7999-8008
-
-
Wang, J.1
Cieplak, P.2
Cai, Q.3
Hsieh, M.-J.4
Wang, J.5
Duan, Y.6
Luo, R.7
-
15
-
-
84962427341
-
Development of Polarizable Models for Molecular Mechanical Calculations II: Induced Dipole Models Significantly Improve Accuracy of Intermolecular Interaction Energies
-
Wang, J.; Cieplak, P.; Li, J.; Wang, J.; Cai, Q.; Hsieh, M.; Lei, H.; Luo, R.; Duan, Y. Development of Polarizable Models for Molecular Mechanical Calculations II: Induced Dipole Models Significantly Improve Accuracy of Intermolecular Interaction Energies J. Phys. Chem. B 2011, 115, 3100-3111
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 3100-3111
-
-
Wang, J.1
Cieplak, P.2
Li, J.3
Wang, J.4
Cai, Q.5
Hsieh, M.6
Lei, H.7
Luo, R.8
Duan, Y.9
-
16
-
-
79953052268
-
Development of Polarizable Models for Molecular Mechanical Calculations I: Parameterization of Atomic Polarizability
-
Wang, J.; Cieplak, P.; Li, J.; Hou, T.; Luo, R.; Duan, Y. Development of Polarizable Models for Molecular Mechanical Calculations I: Parameterization of Atomic Polarizability J. Phys. Chem. B 2011, 115, 3091-3099
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 3091-3099
-
-
Wang, J.1
Cieplak, P.2
Li, J.3
Hou, T.4
Luo, R.5
Duan, Y.6
-
17
-
-
84862654593
-
Development of Polarizable Models for Molecular Mechanical Calculations. 4. Van der Waals Parametrization
-
Wang, J.; Cieplak, P.; Li, J.; Cai, Q.; Hsieh, M.-J.; Luo, R.; Duan, Y. Development of Polarizable Models for Molecular Mechanical Calculations. 4. Van Der Waals Parametrization J. Phys. Chem. B 2012, 116, 7088-7101
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 7088-7101
-
-
Wang, J.1
Cieplak, P.2
Li, J.3
Cai, Q.4
Hsieh, M.-J.5
Luo, R.6
Duan, Y.7
-
18
-
-
84894191473
-
Lipid14: The Amber Lipid Force Field
-
Dickson, C. J.; Madej, B. D.; Skjevik, A. A.; Betz, R. M.; Teigen, K.; Gould, I. R.; Walker, R. C. Lipid14: The Amber Lipid Force Field J. Chem. Theory Comput. 2014, 10, 865-879
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 865-879
-
-
Dickson, C.J.1
Madej, B.D.2
Skjevik, A.A.3
Betz, R.M.4
Teigen, K.5
Gould, I.R.6
Walker, R.C.7
-
19
-
-
0242663237
-
A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-phase Quantum Mechanical Calculations
-
Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. A Point-Charge Force Field for Molecular Mechanics Simulations of Proteins Based on Condensed-phase Quantum Mechanical Calculations J. Comput. Chem. 2003, 24, 1999-2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
-
20
-
-
84902079388
-
Building Force Fields-An Automatic, Systematic and Reproducible Approach
-
Wang, L.-P.; Martínez, T. J.; Pande, V. S. Building Force Fields-An Automatic, Systematic and Reproducible Approach J. Phys. Chem. Lett. 2014, 5, 1885-1891
-
(2014)
J. Phys. Chem. Lett.
, vol.5
, pp. 1885-1891
-
-
Wang, L.-P.1
Martínez, T.J.2
Pande, V.S.3
-
21
-
-
84872142162
-
Systematic Parametrization of Polarizable Force Fields from Quantum Chemistry Data
-
Wang, L.-P.; Chen, J.; Van Voorhis, T. Systematic Parametrization of Polarizable Force Fields From Quantum Chemistry Data J. Chem. Theory Comput. 2012, 9, 452-460
-
(2012)
J. Chem. Theory Comput.
, vol.9
, pp. 452-460
-
-
Wang, L.-P.1
Chen, J.2
Van Voorhis, T.3
-
22
-
-
84860360031
-
Accurate Computation of Gas Uptake in Microporous Organic Molecular Crystals
-
Li, W.; Grimme, S.; Krieg, H.; Möllmann, J.; Zhang, J. Accurate Computation of Gas Uptake in Microporous Organic Molecular Crystals J. Phys. Chem. C 2012, 116, 8865-8871
-
(2012)
J. Phys. Chem. C
, vol.116
, pp. 8865-8871
-
-
Li, W.1
Grimme, S.2
Krieg, H.3
Möllmann, J.4
Zhang, J.5
-
23
-
-
78149265801
-
Accurate Prediction of Hydrogen Adsorption in Metal- Organic Frameworks with Unsaturated Metal Sites via a Combined Density-Functional Theory and Molecular Mechanics Approach
-
Fischer, M.; Kuchta, B.; Firlej, L.; Hoffmann, F.; Fröba, M. Accurate Prediction of Hydrogen Adsorption in Metal- Organic Frameworks with Unsaturated Metal Sites via a Combined Density-Functional Theory and Molecular Mechanics Approach J. Phys. Chem. C 2010, 114, 19116-19126
-
(2010)
J. Phys. Chem. C
, vol.114
, pp. 19116-19126
-
-
Fischer, M.1
Kuchta, B.2
Firlej, L.3
Hoffmann, F.4
Fröba, M.5
-
25
-
-
84866000353
-
Improving Predictions of Gas Adsorption in Metal-Organic Frameworks with Coordinatively Unsaturated Metal Sites: Model Potentials, ab Initio Parameterization, and GCMC Simulations
-
Chen, L.; Morrison, C. A.; Du ren, T. Improving Predictions of Gas Adsorption in Metal-Organic Frameworks with Coordinatively Unsaturated Metal Sites: Model Potentials, ab Initio Parameterization, and GCMC Simulations J. Phys. Chem. C 2012, 116, 18899-18909
-
(2012)
J. Phys. Chem. C
, vol.116
, pp. 18899-18909
-
-
Chen, L.1
Morrison, C.A.2
Du Ren, T.3
-
26
-
-
4444351490
-
Empirical Force Fields for Biological Macromolecules: Overview and Issues
-
Mackerell, A. D. Empirical Force Fields for Biological Macromolecules: Overview and Issues J. Comput. Chem. 2004, 25, 1584-1604
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1584-1604
-
-
Mackerell, A.D.1
-
27
-
-
84874604927
-
Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization
-
Cerutti, D. S.; Rice, J. E.; Swope, W. C.; Case, D. A. Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization J. Phys. Chem. B 2013, 117, 2328-2338
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 2328-2338
-
-
Cerutti, D.S.1
Rice, J.E.2
Swope, W.C.3
Case, D.A.4
-
28
-
-
84898427440
-
Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields
-
Götz, A. W.; Bucher, D.; Lindert, S.; McCammon, J. A. Dipeptide Aggregation in Aqueous Solution from Fixed Point-Charge Force Fields J. Chem. Theory Comput. 2014, 10, 1631-1637
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 1631-1637
-
-
Götz, A.W.1
Bucher, D.2
Lindert, S.3
McCammon, J.A.4
-
30
-
-
0003722376
-
-
Addison-Wesley Publishing Co. Inc. Boston, MA
-
Goldberg, D. E. Genetic Algorithms in Search, Optimization, and Machine Learning; Addison-Wesley Publishing Co., Inc.: Boston, MA, 1989.
-
(1989)
Genetic Algorithms in Search, Optimization, and Machine Learning
-
-
Goldberg, D.E.1
-
32
-
-
33745727034
-
Multi-objective Optimization Using Genetic Algorithms: A Tutorial
-
Konak, A.; Coit, D. W.; Smith, A. E. Multi-objective Optimization Using Genetic Algorithms: A Tutorial Reliab. Eng. Syst. Saf. 2006, 91, 992-1007
-
(2006)
Reliab. Eng. Syst. Saf.
, vol.91
, pp. 992-1007
-
-
Konak, A.1
Coit, D.W.2
Smith, A.E.3
-
33
-
-
84880120844
-
Exploration and Exploitation in Evolutionary Algorithms: A Survey
-
Crepinsek, M.; Liu, S.-H.; Mernik, M. Exploration and Exploitation in Evolutionary Algorithms: A Survey ACM Comput. Surv. 2013, 45, 35
-
(2013)
ACM Comput. Surv.
, vol.45
, pp. 35
-
-
Crepinsek, M.1
Liu, S.-H.2
Mernik, M.3
-
34
-
-
0035451865
-
Automatic Parameterization of Force Field by Systematic Search and Genetic Algorithms
-
Wang, J.; Kollman, P. A. Automatic Parameterization of Force Field by Systematic Search and Genetic Algorithms J. Comput. Chem. 2001, 22, 1219-1228
-
(2001)
J. Comput. Chem.
, vol.22
, pp. 1219-1228
-
-
Wang, J.1
Kollman, P.A.2
-
35
-
-
84923076973
-
Paramfit: Automated Optimization of Force Field Parameters for Molecular Dynamics Simulations
-
Betz, R. M.; Walker, R. C. Paramfit: Automated Optimization of Force Field Parameters for Molecular Dynamics Simulations J. Comput. Chem. 2015, 36, 79-87
-
(2015)
J. Comput. Chem.
, vol.36
, pp. 79-87
-
-
Betz, R.M.1
Walker, R.C.2
-
36
-
-
84887852967
-
Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field
-
Leonarski, F.; Trovato, F.; Tozzini, V.; Les̈, A.; Trylska, J. Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field J. Chem. Theory Comput. 2013, 9, 4874-4889
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 4874-4889
-
-
Leonarski, F.1
Trovato, F.2
Tozzini, V.3
Les̈, A.4
Trylska, J.5
-
37
-
-
84861336877
-
Determination of Best-Fit Potential Parameters for a Reactive Force Field Using a Genetic Algorithm
-
Pahari, P.; Chaturvedi, S. Determination of Best-Fit Potential Parameters for a Reactive Force Field Using a Genetic Algorithm J. Mol. Model. 2012, 18, 1049-1061
-
(2012)
J. Mol. Model.
, vol.18
, pp. 1049-1061
-
-
Pahari, P.1
Chaturvedi, S.2
-
38
-
-
84882661113
-
Global Optimization of Parameters in the Reactive Force Field ReaxFF for SiOH
-
Larsson, H. R.; van Duin, A. C. T.; Hartke, B. Global Optimization of Parameters in the Reactive Force Field ReaxFF for SiOH J. Comput. Chem. 2013, 34, 2178-2189
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 2178-2189
-
-
Larsson, H.R.1
Van Duin, A.C.T.2
Hartke, B.3
-
39
-
-
0037196275
-
MM3 Parametrization of Four- and Five-coordinated Rhenium Complexes by a Genetic Algorithm-Which Factors Influence the Optimization Performance?
-
Strassner, T.; Busold, M.; Herrmann, W. A. MM3 Parametrization of Four- and Five-coordinated Rhenium Complexes by a Genetic Algorithm-Which Factors Influence the Optimization Performance? J. Comput. Chem. 2002, 23, 282-290
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 282-290
-
-
Strassner, T.1
Busold, M.2
Herrmann, W.A.3
-
40
-
-
61949237711
-
Systematic First Principles Parameterization of Force Fields for Metal-Organic Frameworks Using a Genetic Algorithm Approach
-
Tafipolsky, M.; Schmid, R. Systematic First Principles Parameterization of Force Fields for Metal-Organic Frameworks Using a Genetic Algorithm Approach J. Phys. Chem. B 2009, 113, 1341-1352
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 1341-1352
-
-
Tafipolsky, M.1
Schmid, R.2
-
41
-
-
78650093711
-
Optimization of a Molecular Mechanics Force Field for Polyoxometalates Based on a Genetic Algorithm
-
Courcot, B.; Bridgeman, A. J. Optimization of a Molecular Mechanics Force Field for Polyoxometalates Based on a Genetic Algorithm J. Comput. Chem. 2011, 32, 240-247
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 240-247
-
-
Courcot, B.1
Bridgeman, A.J.2
-
42
-
-
17944391259
-
Genetic Algorithm Optimization of a Molecular Mechanics Force Field for Technetium
-
Cundari, T. R.; Fu, W. Genetic Algorithm Optimization of a Molecular Mechanics Force Field for Technetium Inorg. Chim. Acta 2000, 300, 113-124
-
(2000)
Inorg. Chim. Acta
, vol.300
, pp. 113-124
-
-
Cundari, T.R.1
Fu, W.2
-
43
-
-
79953764517
-
Optimization of a Molecular Mechanics Force Field for Type-II Polyoxometalates Focussing on Electrostatic Interactions: A Case Study
-
Courcot, B.; Bridgeman, A. J. Optimization of a Molecular Mechanics Force Field for Type-II Polyoxometalates Focussing on Electrostatic Interactions: A Case Study J. Comput. Chem. 2011, 32, 1703-1710
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 1703-1710
-
-
Courcot, B.1
Bridgeman, A.J.2
-
44
-
-
84986513563
-
Representation of the Molecular Electrostatic Potential by a Net Atomic Charge Model
-
Cox, S. R.; Williams, D. E. Representation of the Molecular Electrostatic Potential by a Net Atomic Charge Model J. Comput. Chem. 1981, 2, 304-323
-
(1981)
J. Comput. Chem.
, vol.2
, pp. 304-323
-
-
Cox, S.R.1
Williams, D.E.2
-
45
-
-
84986468608
-
An Approach to Computing Electrostatic Charges for Molecules
-
Singh, 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, C.1
Kollman, P.A.2
-
46
-
-
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
-
47
-
-
84988098098
-
Atomic Charges Derived from Electrostatic Potentials: A Detailed Study
-
Chirlian, L. E.; Francl, M. M. Atomic Charges Derived From Electrostatic Potentials: A Detailed Study J. Comput. Chem. 1987, 8, 894-905
-
(1987)
J. Comput. Chem.
, vol.8
, pp. 894-905
-
-
Chirlian, L.E.1
Francl, M.M.2
-
48
-
-
84986513567
-
Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials. the Need for High Sampling Density in Formamide Conformational Analysis
-
Breneman, C. M.; Wiberg, K. B. Determining Atom-Centered Monopoles From Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis J. Comput. Chem. 1990, 11, 361-373
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 361-373
-
-
Breneman, C.M.1
Wiberg, K.B.2
-
49
-
-
0342877286
-
Determination of Partial Atomic Charges from ab Initio Molecular Electrostatic Potentials. Application to Formamide, Methanol, and Formic Acid
-
Momany, F. A. Determination of Partial Atomic Charges From ab Initio Molecular Electrostatic Potentials. Application to Formamide, Methanol, and Formic Acid J. Phys. Chem. 1978, 82, 592-601
-
(1978)
J. Phys. Chem.
, vol.82
, pp. 592-601
-
-
Momany, F.A.1
-
50
-
-
84900822803
-
Multipolar Electrostatics
-
Cardamone, S.; Hughes, T. J.; Popelier, P. L. A. Multipolar Electrostatics Phys. Chem. Chem. Phys. 2014, 16, 10367-10387
-
(2014)
Phys. Chem. Chem. Phys.
, vol.16
, pp. 10367-10387
-
-
Cardamone, S.1
Hughes, T.J.2
Popelier, P.L.A.3
-
51
-
-
84907993281
-
Charge Anisotropy: Where Atomic Multipoles Matter Most
-
Kramer, C.; Spinn, A.; Liedl, K. R. Charge Anisotropy: Where Atomic Multipoles Matter Most J. Chem. Theory Comput. 2014, 10, 4488-4496
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 4488-4496
-
-
Kramer, C.1
Spinn, A.2
Liedl, K.R.3
-
52
-
-
84986468508
-
Derivation of Net Atomic Charges from Molecular Electrostatic Potentials
-
Woods, R. J.; Khalil, M.; Pell, W.; Moffat, S. H.; Smith, V. H. Derivation of Net Atomic Charges From Molecular Electrostatic Potentials J. Comput. Chem. 1990, 11, 297-310
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 297-310
-
-
Woods, R.J.1
Khalil, M.2
Pell, W.3
Moffat, S.H.4
Smith, V.H.5
-
53
-
-
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
-
54
-
-
1142291803
-
Rules for Minimal Atomic Multipole Expansion of Molecular Fields
-
Tsiper, E. V.; Burke, K. Rules for Minimal Atomic Multipole Expansion of Molecular Fields J. Chem. Phys. 2004, 120, 1153-1156
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 1153-1156
-
-
Tsiper, E.V.1
Burke, K.2
-
55
-
-
84916613769
-
Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space
-
Jakobsen, S.; Jensen, F. Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space J. Chem. Theory Comput. 2014, 10, 5493-5504
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 5493-5504
-
-
Jakobsen, S.1
Jensen, F.2
-
56
-
-
0001516994
-
Conformational Dependence of Electrostatic Potential-Derived Charges: Studies of the Fitting Procedure
-
Stouch, T. R.; Williams, D. E. Conformational Dependence of Electrostatic Potential-Derived Charges: Studies of the Fitting Procedure J. Comput. Chem. 1993, 14, 858-866
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 858-866
-
-
Stouch, T.R.1
Williams, D.E.2
-
57
-
-
84986437311
-
Conformational Dependence of Electrostatic Potential Derived Charges of a Lipid Headgroup: Glycerylphosphorylcholine
-
Stouch, T. R.; Williams, D. E. Conformational Dependence of Electrostatic Potential Derived Charges of a Lipid Headgroup: Glycerylphosphorylcholine J. Comput. Chem. 1992, 13, 622-632
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 622-632
-
-
Stouch, T.R.1
Williams, D.E.2
-
58
-
-
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.; 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.3
Kollman, P.A.4
-
59
-
-
0343380162
-
Charges Fit to Electrostatic Potentials. 11. 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. 11. 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
-
60
-
-
0000667030
-
Application of RESP Charges to Calculate Conformational Energies, Hydrogen Bond Energies, and Free Energies of Solvation
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollmann, P. A. Application of RESP Charges to Calculate Conformational Energies, Hydrogen Bond Energies, and Free Energies of Solvation J. Am. Chem. Soc. 1993, 115, 9620-9631
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9620-9631
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollmann, P.A.4
-
61
-
-
0001632356
-
A Potential Function for Computer Simulation Studies of Proton Transfer in Acetylacetone
-
Hinsen, K.; Roux, B. A Potential Function for Computer Simulation Studies of Proton Transfer in Acetylacetone J. Comput. Chem. 1997, 18, 368-380
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 368-380
-
-
Hinsen, K.1
Roux, B.2
-
62
-
-
27944511812
-
An Optimal Point-Charge Model for Molecular Electrostatic Potentials
-
Simmonett, A. C.; Gilbert, A. T.; Gill, P. M. An Optimal Point-Charge Model for Molecular Electrostatic Potentials Mol. Phys. 2005, 103, 2789-2793
-
(2005)
Mol. Phys.
, vol.103
, pp. 2789-2793
-
-
Simmonett, A.C.1
Gilbert, A.T.2
Gill, P.M.3
-
63
-
-
84890110473
-
Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting
-
Burger, S. K.; Schofield, J.; Ayers, P. W. Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting. J. Phys. Chem. B 2013,.
-
(2013)
J. Phys. Chem. B
-
-
Burger, S.K.1
Schofield, J.2
Ayers, P.W.3
-
64
-
-
33645511814
-
A New Force Field (ECEPP-05) for Peptides, Proteins, and Organic Molecules
-
Arnautova, Y. A.; Jagielska, A.; Scheraga, H. A. A New Force Field (ECEPP-05) for Peptides, Proteins, and Organic Molecules J. Phys. Chem. B 2006, 110, 5025-5044
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 5025-5044
-
-
Arnautova, Y.A.1
Jagielska, A.2
Scheraga, H.A.3
-
65
-
-
84875225459
-
A Numerically Stable Restrained Electrostatic Potential Charge Fitting Method
-
Zeng, J.; Duan, L.; Zhang, J. Z. H.; Mei, Y. A Numerically Stable Restrained Electrostatic Potential Charge Fitting Method J. Comput. Chem. 2013, 34, 847-853
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 847-853
-
-
Zeng, J.1
Duan, L.2
Zhang, J.Z.H.3
Mei, Y.4
-
66
-
-
84882446110
-
Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on ab Initio Target Data
-
Huang, L.; Roux, B. Automated Force Field Parameterization for Nonpolarizable and Polarizable Atomic Models Based on ab Initio Target Data J. Chem. Theory Comput. 2013, 9, 3543-3556
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3543-3556
-
-
Huang, L.1
Roux, B.2
-
67
-
-
84879104663
-
Fast and Accurate Generation of ab Initio Quality Atomic Charges Using Nonparametric Statistical Regression
-
Rai, B. K.; Bakken, G. A. Fast and Accurate Generation of ab Initio Quality Atomic Charges Using Nonparametric Statistical Regression J. Comput. Chem. 2013, 34, 1661-1671
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 1661-1671
-
-
Rai, B.K.1
Bakken, G.A.2
-
68
-
-
39049147617
-
GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates
-
Kirschner, K. N.; Yongye, A. B.; Tschampel, S. M.; González-Outeiriño, J.; Daniels, C. R.; Foley, B. L.; Woods, R. J. GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates J. Comput. Chem. 2008, 29, 622-655
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 622-655
-
-
Kirschner, K.N.1
Yongye, A.B.2
Tschampel, S.M.3
González-Outeiriño, J.4
Daniels, C.R.5
Foley, B.L.6
Woods, R.J.7
-
69
-
-
38749099020
-
Approach for the Simulation and Modeling of Flexible Rings: Application to the A-d-Arabinofuranoside Ring, a Key Constituent of Polysaccharides from Mycobacterium tuberculosis
-
Seo, M.; Castillo, N.; Ganzynkowicz, R.; Daniels, C. R.; Woods, R. J.; Lowary, T. L.; Roy, P.-N. Approach for the Simulation and Modeling of Flexible Rings: Application to the A-d-Arabinofuranoside Ring, a Key Constituent of Polysaccharides from Mycobacterium tuberculosis J. Chem. Theory Comput. 2008, 4, 184-191
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 184-191
-
-
Seo, M.1
Castillo, N.2
Ganzynkowicz, R.3
Daniels, C.R.4
Woods, R.J.5
Lowary, T.L.6
Roy, P.-N.7
-
70
-
-
84986516411
-
Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers Charge Derivation for DNA, RNA, and Proteins
-
Cieplak, P.; Cornell, W. D.; Bayly, C.; Kollman, P. A. Application of the Multimolecule and Multiconformational RESP Methodology to Biopolymers Charge Derivation for DNA, RNA, and Proteins J. Comput. Chem. 1995, 16, 1357-1377
-
(1995)
J. Comput. Chem.
, vol.16
, pp. 1357-1377
-
-
Cieplak, P.1
Cornell, W.D.2
Bayly, C.3
Kollman, P.A.4
-
71
-
-
77954566051
-
The R.E.D. Tools: Advances in RESP and ESP Charge Derivation and Force Field Library Building
-
Dupradeau, F.-Y.; Pigache, A.; Zaffran, T.; Savineau, C.; Lelong, R.; Grivel, N.; Lelong, D.; Rosanski, W.; Cieplak, P. The R.E.D. Tools: Advances in RESP and ESP Charge Derivation and Force Field Library Building Phys. Chem. Chem. Phys. 2010, 12, 7821-7839
-
(2010)
Phys. Chem. Chem. Phys.
, vol.12
, pp. 7821-7839
-
-
Dupradeau, F.-Y.1
Pigache, A.2
Zaffran, T.3
Savineau, C.4
Lelong, R.5
Grivel, N.6
Lelong, D.7
Rosanski, W.8
Cieplak, P.9
-
72
-
-
84877697866
-
Scoring Multipole Electrostatics in Condensed-Phase Atomistic Simulations
-
Bereau, T.; Kramer, C.; Monnard, F. W.; Nogueira, E. S.; Ward, T. R.; Meuwly, M. Scoring Multipole Electrostatics in Condensed-Phase Atomistic Simulations J. Phys. Chem. B 2013, 117, 5460-5471
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 5460-5471
-
-
Bereau, T.1
Kramer, C.2
Monnard, F.W.3
Nogueira, E.S.4
Ward, T.R.5
Meuwly, M.6
-
73
-
-
84888361579
-
Toward Force Fields for Atomistic Simulations of Iridium-Containing Complexes
-
Hofmann, F. D.; Devereux, M.; Pfaltz, A.; Meuwly, M. Toward Force Fields for Atomistic Simulations of Iridium-Containing Complexes J. Comput. Chem. 2013, 35, 18-29
-
(2013)
J. Comput. Chem.
, vol.35
, pp. 18-29
-
-
Hofmann, F.D.1
Devereux, M.2
Pfaltz, A.3
Meuwly, M.4
-
74
-
-
0037173897
-
D-RESP: Dynamically Generated Electrostatic Potential Derived Charges from Quantum Mechanics/Molecular Mechanics Simulations
-
Laio, A.; VandeVondele, J.; Rothlisberger, U. D-RESP: Dynamically Generated Electrostatic Potential Derived Charges From Quantum Mechanics/Molecular Mechanics Simulations J. Phys. Chem. B 2002, 106, 7300-7307
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 7300-7307
-
-
Laio, A.1
Vandevondele, J.2
Rothlisberger, U.3
-
75
-
-
3042554016
-
A Variational Definition of Electrostatic Potential Derived Charges
-
Laio, A.; Gervasio, F. L.; VandeVondele, J.; Sulpizi, M.; Rothlisberger, U. A Variational Definition of Electrostatic Potential Derived Charges J. Phys. Chem. B 2004, 108, 7963-7968
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 7963-7968
-
-
Laio, A.1
Gervasio, F.L.2
Vandevondele, J.3
Sulpizi, M.4
Rothlisberger, U.5
-
76
-
-
84916232194
-
AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations
-
Graen, T. M. D.; Hoefling, M.; Grubmüller, H. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations J. Chem. Theory Comput. 2014, 10, 5505-5512
-
(2014)
J. Chem. Theory Comput.
, vol.10
, pp. 5505-5512
-
-
Graen, T.M.D.1
Hoefling, M.2
Grubmüller, H.3
-
77
-
-
84906510049
-
The Influence of Ser-154, Cys-113, and the Phosphorylated Threonine Residue on the Catalytic Reaction Mechanism of Pin1
-
Vöhringer-Martinez, E.; Verstraelen, T.; Ayers, P. W. The Influence of Ser-154, Cys-113, and the Phosphorylated Threonine Residue on the Catalytic Reaction Mechanism of Pin1 J. Phys. Chem. B 2014, 118, 9871-9880
-
(2014)
J. Phys. Chem. B
, vol.118
, pp. 9871-9880
-
-
Vöhringer-Martinez, E.1
Verstraelen, T.2
Ayers, P.W.3
-
78
-
-
0000189651
-
Density-Functional Thermochemistry. III. the Role of Exact Exchange
-
Becke, A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange J. Chem. Phys. 1993, 98, 5648-5652
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
79
-
-
33751157732
-
Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields
-
Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields J. Phys. Chem. 1994, 98, 11623-11627
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 11623-11627
-
-
Stephens, P.J.1
Devlin, F.J.2
Chabalowski, C.F.3
Frisch, M.J.4
-
80
-
-
70450206724
-
-
revision C.01; Gaussian, Inc. Wallingford, CT
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Gaussian 09, revision C.01; Gaussian, Inc.: Wallingford, CT, 2010.
-
(2010)
Gaussian 09
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.A.10
-
82
-
-
0000308566
-
Real-Coded Genetic Algorithms and Interval-Schemata
-
In; Whitely, D. Morgan Kaufmann Publishers, Inc. San Manteo, CA
-
Eshelman, L. J.; David, S. Real-Coded Genetic Algorithms and Interval-Schemata. In Foundations of Genetic Algorithms; Whitely, D., Ed.; Morgan Kaufmann Publishers, Inc.: San Manteo, CA, 1993; pp 187-202.
-
(1993)
Foundations of Genetic Algorithms
, pp. 187-202
-
-
Eshelman, L.J.1
David, S.2
-
83
-
-
0032136585
-
Tackling Real-Coded Genetic Algorithms: Operators and Tools for Behavioural Analysis
-
Herrera, F.; Lozano, M.; Verdegay, J. L. Tackling Real-Coded Genetic Algorithms: Operators and Tools for Behavioural Analysis Artif. Intell. Rev. 1998, 12, 265-319
-
(1998)
Artif. Intell. Rev.
, vol.12
, pp. 265-319
-
-
Herrera, F.1
Lozano, M.2
Verdegay, J.L.3
-
84
-
-
0000332101
-
Real-Coded Genetic Algorithms, Virtual Alphabets, and Blocking
-
Goldberg, D. E. Real-Coded Genetic Algorithms, Virtual Alphabets, and Blocking Complex Syst. 1991, 5, 139-167
-
(1991)
Complex Syst.
, vol.5
, pp. 139-167
-
-
Goldberg, D.E.1
-
85
-
-
79952595565
-
The NumPy Array: A Structure for Efficient Numerical Computation
-
Van Der Walt, S.; Colbert, S. C.; Varoquaux, G. The NumPy Array: A Structure for Efficient Numerical Computation Comput. Sci. Eng. 2011, 13, 22-30
-
(2011)
Comput. Sci. Eng.
, vol.13
, pp. 22-30
-
-
Van Der Walt, S.1
Colbert, S.C.2
Varoquaux, G.3
-
87
-
-
34248143032
-
Covariance Matrix Adaptation for Multi-objective Optimization
-
Igel, C.; Hansen, N.; Roth, S. Covariance Matrix Adaptation for Multi-objective Optimization Evol. Comput. 2007, 15, 1-28
-
(2007)
Evol. Comput.
, vol.15
, pp. 1-28
-
-
Igel, C.1
Hansen, N.2
Roth, S.3
-
88
-
-
0042879997
-
Reducing the Time Complexity of the Derandomized Evolution Strategy with Covariance Matrix Adaptation (CMA-ES)
-
Hansen, N.; Müller, S. D.; Koumoutsakos, P. Reducing the Time Complexity of the Derandomized Evolution Strategy with Covariance Matrix Adaptation (CMA-ES) Evol. Comput. 2003, 11, 1-18
-
(2003)
Evol. Comput.
, vol.11
, pp. 1-18
-
-
Hansen, N.1
Müller, S.D.2
Koumoutsakos, P.3
-
89
-
-
0035377566
-
Completely Derandomized Self-Adaptation in Evolution Strategies
-
Hansen, N.; Ostermeier, A. Completely Derandomized Self-Adaptation in Evolution Strategies Evol. Comput. 2001, 9, 159-195
-
(2001)
Evol. Comput.
, vol.9
, pp. 159-195
-
-
Hansen, N.1
Ostermeier, A.2
-
90
-
-
33845271655
-
The CMA Evolution Strategy: A Comparing Review
-
In; Lozano, J. Larrañaga, P. Inza, I. Bengoetxea, E. Springer: Berlin Heidelberg
-
Hansen, N. The CMA Evolution Strategy: A Comparing Review. In Towards a New Evolutionary Computation; Lozano, J.; Larrañaga, P.; Inza, I.; Bengoetxea, E., Eds.; Springer: Berlin Heidelberg, 2006; pp 75-102.
-
(2006)
Towards A New Evolutionary Computation
, pp. 75-102
-
-
Hansen, N.1
-
91
-
-
34247493236
-
Matplotlib: A 2D Graphics Environment
-
Hunter, J. D. Matplotlib: A 2D Graphics Environment Comput. Sci. Eng. 2007, 9, 0090-0095
-
(2007)
Comput. Sci. Eng.
, vol.9
, pp. 0090-0095
-
-
Hunter, J.D.1
-
92
-
-
0029768771
-
Re-evaluating Genetic Algorithm Performance under Coordinate Rotation of Benchmark Functions. A Survey of Some Theoretical and Practical Aspects of Genetic Algorithms
-
Salomon, R. Re-evaluating Genetic Algorithm Performance under Coordinate Rotation of Benchmark Functions. A Survey of Some Theoretical and Practical Aspects of Genetic Algorithms BioSystems 1996, 39, 263-278
-
(1996)
BioSystems
, vol.39
, pp. 263-278
-
-
Salomon, R.1
-
94
-
-
84902978469
-
Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields
-
Debiec, K. T.; Gronenborn, A. M.; Chong, L. T. Evaluating the Strength of Salt Bridges: A Comparison of Current Biomolecular Force Fields J. Phys. Chem. B 2014, 118, 6561-6569
-
(2014)
J. Phys. Chem. B
, vol.118
, pp. 6561-6569
-
-
Debiec, K.T.1
Gronenborn, A.M.2
Chong, L.T.3
|