-
1
-
-
0017251977
-
Bicycle-pedal model for the first step in the vision process
-
Warshel A. Bicycle-pedal model for the first step in the vision process. Nature 1976;260:679-683.
-
(1976)
Nature
, vol.260
, pp. 679-683
-
-
Warshel, A.1
-
2
-
-
0012608253
-
Molecular Dynamics Study of the Bovine Pancreatic Trypsin Inhibitor
-
Berendsen HJC, editor. Models for protein dynamics. CECAM, Université de Paris IX Orsay, France;
-
McCammon JA. Molecular Dynamics Study of the Bovine Pancreatic Trypsin Inhibitor, in "Report of the 1976 Workshop, Models for Protein Dynamics" Berendsen HJC, editor. Models for protein dynamics. CECAM, Université de Paris IX Orsay, France; 1976. p 137.
-
(1976)
Report of the 1976 Workshop, Models for Protein Dynamics
, pp. 137
-
-
McCammon, J.A.1
-
4
-
-
84962383158
-
Molecular dynamic simulations of nucleic acids
-
New York: Wiley (in press)
-
Orozco M, Rueda M, Blas JR, Cubero E, Luque FJ, Laughton CA. Molecular dynamic simulations of nucleic acids. In: Encyclopedia of Computational Chemistry. New York: Wiley (in press).
-
Encyclopedia of Computational Chemistry
-
-
Orozco, M.1
Rueda, M.2
Blas, J.R.3
Cubero, E.4
Luque, F.J.5
Laughton, C.A.6
-
5
-
-
1242347628
-
Theoretical Methods for the Simulation of Nucleic Acids
-
Orozco M, Pérez A, Noy A, Luque FJ. Theoretical Methods for the Simulation of Nucleic Acids. Chem Soc Rev 2003; 32:350-364
-
(2003)
Chem Soc Rev
, vol.32
, pp. 350-364
-
-
Orozco, M.1
Pérez, A.2
Noy, A.3
Luque, F.J.4
-
7
-
-
0034979318
-
Biomolecular simulations: Recent developments in force-fields simulations of enzyme catalysis protein-ligand protein-protein and protein-nucleic acid noncovalent interactions
-
Wang W, Donini O, Reyes CM, Kollman PA. Biomolecular simulations: recent developments in force-fields simulations of enzyme catalysis protein-ligand protein-protein and protein-nucleic acid noncovalent interactions. Annu Rev Biophys Biomol Struct 2001;30:211-243.
-
(2001)
Annu Rev Biophys Biomol Struct
, vol.30
, pp. 211-243
-
-
Wang, W.1
Donini, O.2
Reyes, C.M.3
Kollman, P.A.4
-
8
-
-
2542564912
-
Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules
-
Kollman PA. Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules. Acc Chem Res 1996;29:461-469.
-
(1996)
Acc Chem Res
, vol.29
, pp. 461-469
-
-
Kollman, P.A.1
-
9
-
-
0033654654
-
Molecular dynamics simulation of nucleic acids
-
Cheatham TE, Kollman PA. Molecular dynamics simulation of nucleic acids. Ann Rev Phys Chem 2000;51:435-471.
-
(2000)
Ann Rev Phys Chem
, vol.51
, pp. 435-471
-
-
Cheatham, T.E.1
Kollman, P.A.2
-
10
-
-
0026556022
-
On the interpretation of biochemical data by molecular dynamics computer simulation
-
Van Gunsteren WF, Mark AE. On the interpretation of biochemical data by molecular dynamics computer simulation. Eur J Biochem 1992;204:947-961.
-
(1992)
Eur J Biochem
, vol.204
, pp. 947-961
-
-
Van Gunsteren, W.F.1
Mark, A.E.2
-
11
-
-
2142813682
-
Computer simulation of molecular dynamics: Methodology applications and perspectives in chemistry
-
Van Gunsteren WF, Berendsen HJ. Computer simulation of molecular dynamics: methodology applications and perspectives in chemistry. Angew Che Int Ed Engl 1990;29:992-1023.
-
(1990)
Angew Che Int Ed Engl
, vol.29
, pp. 992-1023
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.2
-
12
-
-
0025048105
-
Molecular dynamics simulations in biology
-
Karplus M, Petsko GA. Molecular dynamics simulations in biology. Nature 1990;347:631-639.
-
(1990)
Nature
, vol.347
, pp. 631-639
-
-
Karplus, M.1
Petsko, G.A.2
-
13
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nature Struct Biol 2002;9:646-652.
-
(2002)
Nature Struct Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
15
-
-
0034314630
-
Theoretical methods for the description of the solvent effect in biomolecular systems
-
Orozco M, Luque PJ. Theoretical methods for the description of the solvent effect in biomolecular systems. Chem Rev 2000;100:4187-4225.
-
(2000)
Chem Rev
, vol.100
, pp. 4187-4225
-
-
Orozco, M.1
Luque, P.J.2
-
16
-
-
0035828630
-
On the calculation of entropy from covariance matrices of the atomic fluctuations
-
Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys 2001;115:6289-6292.
-
(2001)
J Chem Phys
, vol.115
, pp. 6289-6292
-
-
Andricioaei, I.1
Karplus, M.2
-
17
-
-
0001351515
-
Estimation of absolute and relative entropies of macromolecules using the covariance matrix
-
Schlitter J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem Phys Let 1993;215:617-621.
-
(1993)
Chem Phys Let
, vol.215
, pp. 617-621
-
-
Schlitter, J.1
-
18
-
-
0035915354
-
Cooperativity in drug-DNA recognition: A molecular dynamics study
-
Harris SA, Gavathiotis E, Searle MS, Orozco M, Laughton CA. Cooperativity in drug-DNA recognition: a molecular dynamics study. J Am Chem Soc 2001;123:12658-12663.
-
(2001)
J Am Chem Soc
, vol.123
, pp. 12658-12663
-
-
Harris, S.A.1
Gavathiotis, E.2
Searle, M.S.3
Orozco, M.4
Laughton, C.A.5
-
19
-
-
0034323089
-
Absolute entropies from molecular dynamics simulation trajectories
-
Schafer H, Mark AE, van Gunsteren WF. Absolute entropies from molecular dynamics simulation trajectories. J Chem Phys 2000;113:7809-7817.
-
(2000)
J Chem Phys
, vol.113
, pp. 7809-7817
-
-
Schafer, H.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
20
-
-
0000408363
-
Approximate atomic surfaces from linear combination of pairwise overlaps (LCPO)
-
Weiser J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combination of pairwise overlaps (LCPO). J Comp Chem 1999;20:217-230.
-
(1999)
J Comp Chem
, vol.20
, pp. 217-230
-
-
Weiser, J.1
Shenkin, P.S.2
Still, W.C.3
-
21
-
-
0023779259
-
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies binding energies and conformational analysis
-
Gilson MK, Honig B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies binding energies and conformational analysis. Proteins 1988;4:7-18.
-
(1988)
Proteins
, vol.4
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
22
-
-
4243463817
-
Electrostatics in biomolecular structure and dynamics
-
Davis ME, McCammon JA. Electrostatics in biomolecular structure and dynamics. Chem Rev 1990;90:509-521.
-
(1990)
Chem Rev
, vol.90
, pp. 509-521
-
-
Davis, M.E.1
McCammon, J.A.2
-
23
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still WC, Tempczyk A, Hawley RC, Hendrickson T. Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 1990; 112:6127-6129.
-
(1990)
J Am Chem Soc
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
24
-
-
0032560959
-
Continuum solvent studies of the stability of DNA RNA and phosphoramidate-DNA helices
-
Srinivasan J, Cheatham TE, Kollman PA, Case DA. Continuum solvent studies of the stability of DNA RNA and phosphoramidate-DNA helices. J Am Chem Soc 1998;120:9401-9409.
-
(1998)
J Am Chem Soc
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham, T.E.2
Kollman, P.A.3
Case, D.A.4
-
25
-
-
0034212858
-
Use of MM/PB/SA in estimating the free energies of proteins: Application to native intermediates and unfolded vilin headpiece
-
Lee MR, Duan Y, Kollman PA. Use of MM/PB/SA in estimating the free energies of proteins: application to native intermediates and unfolded vilin headpiece. Proteins 2000;39:309-316.
-
(2000)
Proteins
, vol.39
, pp. 309-316
-
-
Lee, M.R.1
Duan, Y.2
Kollman, P.A.3
-
26
-
-
0034521981
-
Calculating the structure and free energies of complex molecules: Combining molecular mechanics and continuum models
-
Kollman PA, 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 DA, Cheatham TE. Calculating the structure and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 2000;33:889-897.
-
(2000)
Acc Chem Res
, vol.33
, 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
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
27
-
-
0035814387
-
Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes
-
Cubero E, Luque FJ, Orozco M. Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes. JAm Chem Soc 2001;123:12018-12025.
-
(2001)
JAm Chem Soc
, vol.123
, pp. 12018-12025
-
-
Cubero, E.1
Luque, F.J.2
Orozco, M.3
-
28
-
-
0344875160
-
Theoretical study of a new DNA structure: The antiparallel Hoogsteen duplex
-
Cubero E, Abrescia NGA, Subirana JA, Luque FJ, Orozco M. Theoretical study of a new DNA structure: the antiparallel Hoogsteen duplex. J Am Chem Soc 2003;125:14603-14612.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 14603-14612
-
-
Cubero, E.1
Abrescia, N.G.A.2
Subirana, J.A.3
Luque, F.J.4
Orozco, M.5
-
30
-
-
11744256643
-
Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
-
Tomasi J, Persico M. Molecular interactions in solution: an overview of methods based on continuous distributions of the solvent. Chem Rev 1994;94: 2027-2094.
-
(1994)
Chem Rev
, vol.94
, pp. 2027-2094
-
-
Tomasi, J.1
Persico, M.2
-
31
-
-
84961981091
-
Implicit solvation models: Equilibria structure spectra and dynamics
-
Cramer CJ, Truhlar DF. Implicit solvation models: equilibria structure spectra and dynamics. Chem Rev 1999;99:2161-2200.
-
(1999)
Chem Rev
, vol.99
, pp. 2161-2200
-
-
Cramer, C.J.1
Truhlar, D.F.2
-
32
-
-
84962415061
-
Continuum solvation models: Dissecting the free energy of solvation
-
Luque FJ, Curutchet C, Muñoz-Muriedas J, Bidon-Chanal A, Soteras I, Morreale A , Gelpí JL, Orozco M. Continuum solvation models: Dissecting the free energy of solvation. Phys Chem Chem Phys 2003;5:3827-3836.
-
(2003)
Phys Chem Chem Phys
, vol.5
, pp. 3827-3836
-
-
Luque, F.J.1
Curutchet, C.2
Muñoz-Muriedas, J.3
Bidon-Chanal, A.4
Soteras, I.5
Morreale, A.6
Gelpí, J.L.7
Orozco, M.8
-
34
-
-
84962439423
-
Electrostatic component of solvation comparison of SCRF continuum models
-
Curutchet C, Cramer CJ, Truhlar DG, Ruiz-López MF, Rinaldi D, Orozco M, Luque FJ. Electrostatic component of solvation comparison of SCRF continuum models. J Comp Chem 2003;24:284-297.
-
(2003)
J Comp Chem
, vol.24
, pp. 284-297
-
-
Curutchet, C.1
Cramer, C.J.2
Truhlar, D.G.3
Ruiz-López, M.F.4
Rinaldi, D.5
Orozco, M.6
Luque, F.J.7
-
35
-
-
0035425603
-
Solvation in octanol: Parametrization of the continuum MST model
-
Curutchet C, Orozco M, Luque FJ. Solvation in octanol: parametrization of the continuum MST model. J Comp Chem 2001;22:1180-1193.
-
(2001)
J Comp Chem
, vol.22
, pp. 1180-1193
-
-
Curutchet, C.1
Orozco, M.2
Luque, F.J.3
-
36
-
-
0025891413
-
Electrostatic energy and macromolecular function
-
Warshel J, Aqvist J. Electrostatic energy and macromolecular function. Annu Rev Biophys Biophys Chem 1991;20:267-298.
-
(1991)
Annu Rev Biophys Biophys Chem
, vol.20
, pp. 267-298
-
-
Warshel, J.1
Aqvist, J.2
-
37
-
-
0035451052
-
What are the dielectric "constants" of proteins and how to validate electrostatic models?
-
Schutz CN, Warshel A. What are the dielectric "constants" of proteins and how to validate electrostatic models? Proteins 2001;44:400-417.
-
(2001)
Proteins
, vol.44
, pp. 400-417
-
-
Schutz, C.N.1
Warshel, A.2
-
38
-
-
0021480222
-
Macroscopic models for studies of electrostatic interactions in proteins: Limitations and applicability
-
Warshel A, Russell ST, Churg AK. Macroscopic models for studies of electrostatic interactions in proteins: limitations and applicability. Proc Natl Acad Sci USA 1984;81:4785-4789.
-
(1984)
Proc Natl Acad Sci USA
, vol.81
, pp. 4785-4789
-
-
Warshel, A.1
Russell, S.T.2
Churg, A.K.3
-
39
-
-
0000728542
-
Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs
-
Lee FS, Chu ZT, Warshel A. Microscopic and semimicroscopic calculations of electrostatic energies in proteins by the POLARIS and ENZYMIX programs. J Comp Chem 1993;14:161-185.
-
(1993)
J Comp Chem
, vol.14
, pp. 161-185
-
-
Lee, F.S.1
Chu, Z.T.2
Warshel, A.3
-
40
-
-
0026596911
-
Calculations of antibody-antigen interactions: Microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603
-
Lee FS, Chu ZT, Bolger MB, Warshel A. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. Prot Eng 1992;5:215-228.
-
(1992)
Prot Eng
, vol.5
, pp. 215-228
-
-
Lee, F.S.1
Chu, Z.T.2
Bolger, M.B.3
Warshel, A.4
-
41
-
-
0021476470
-
Calculations of electrostatic interactions in biological systems and in solutions
-
Warshel A, Rusell ST. Calculations of electrostatic interactions in biological systems and in solutions. Q Rev Biophys 1984;17:283-422.
-
(1984)
Q Rev Biophys
, vol.17
, pp. 283-422
-
-
Warshel, A.1
Rusell, S.T.2
-
42
-
-
0000763912
-
Molecular basis for the Born model of ion solvation
-
Roux B, Yu HA, Karplus M. Molecular basis for the Born model of ion solvation. J Phys Chem 1990;94:4683-4688.
-
(1990)
J Phys Chem
, vol.94
, pp. 4683-4688
-
-
Roux, B.1
Yu, H.A.2
Karplus, M.3
-
43
-
-
0000354626
-
Investigation of the free-energy functions for electron-transfer reactions
-
King U, Warshel A. Investigation of the free-energy functions for electron-transfer reactions. J Chem Phys 1990;93:8682-8692.
-
(1990)
J Chem Phys
, vol.93
, pp. 8682-8692
-
-
King, U.1
Warshel, A.2
-
44
-
-
0000789127
-
Linear free energy relationships with quantum mechanical corrections: Classical and quantum mechanical rate constants for hydride transfer between NAD+ analogs in solutions
-
Kong YS, Warshel A. Linear free energy relationships with quantum mechanical corrections: classical and quantum mechanical rate constants for hydride transfer between NAD+ analogs in solutions. J Am Chem Soc 1995;117:6234-6242.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 6234-6242
-
-
Kong, Y.S.1
Warshel, A.2
-
45
-
-
0344796204
-
Ion water interaction potentials derived from free-energy perturbation simulations
-
Aqvist J. Ion water interaction potentials derived from free-energy perturbation simulations. J Phys Chem 1990;94:8021-8024.
-
(1990)
J Phys Chem
, vol.94
, pp. 8021-8024
-
-
Aqvist, J.1
-
46
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Aqvist J, Medina C, Samuelsson JE. A new method for predicting binding affinity in computer-aided drug design. Prot Eng 1994;7:385-391.
-
(1994)
Prot Eng
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
47
-
-
0030134110
-
Validity of electrostatic linear response in polar solvents
-
Aqvist J, Hansson T. Validity of electrostatic linear response in polar solvents. J Phys Chem 1996;100:9512-9521.
-
(1996)
J Phys Chem
, vol.100
, pp. 9512-9521
-
-
Aqvist, J.1
Hansson, T.2
-
48
-
-
84962407457
-
The polarization contribution to the free energy of hydration
-
Orozco M, Luque FJ, Habibolahzadeh D, Gao J. The polarization contribution to the free energy of hydration. J Chem Phys 1995;102:6145-6152.
-
(1995)
J Chem Phys
, vol.102
, pp. 6145-6152
-
-
Orozco, M.1
Luque, F.J.2
Habibolahzadeh, D.3
Gao, J.4
-
49
-
-
0001389474
-
An extended linear response method for determining free energies of hydration
-
Carlson HA, Jorgensen WL. An extended linear response method for determining free energies of hydration. J Phys Chem 1995;99:10667-10673.
-
(1995)
J Phys Chem
, vol.99
, pp. 10667-10673
-
-
Carlson, H.A.1
Jorgensen, W.L.2
-
50
-
-
0035966872
-
Estimation of binding affinities for selective thrombin inhibitors via Monte Carlo simulations
-
Pierce AC, Jorgensen WL. Estimation of binding affinities for selective thrombin inhibitors via Monte Carlo simulations. J Med Chem 2001;44:1043-1050.
-
(2001)
J Med Chem
, vol.44
, pp. 1043-1050
-
-
Pierce, A.C.1
Jorgensen, W.L.2
-
51
-
-
0037059913
-
Estimation of binding affinities for celecoxib analogues with COX-2 via Monte Carlo-extended linear response
-
Wesolowski SS, Jorgensen WL. Estimation of binding affinities for celecoxib analogues with COX-2 via Monte Carlo-extended linear response. Bioorg Med Chem Lett 2002;12:267-270.
-
(2002)
Bioorg Med Chem Lett
, vol.12
, pp. 267-270
-
-
Wesolowski, S.S.1
Jorgensen, W.L.2
-
52
-
-
5544264558
-
Gaussian fluctuation formula for electrostatic free-energy changes in solution
-
Levy R.M, Belhadj M, Kitchen, D.E. Gaussian fluctuation formula for electrostatic free-energy changes in solution. J Chem Phys 1991;3627-3633.
-
(1991)
J Chem Phys
, pp. 3627-3633
-
-
Levy, R.M.1
Belhadj, M.2
Kitchen, D.E.3
-
53
-
-
84962467269
-
Molecular model for aqueous ferrous-ferric electron transfer
-
Kuharsi R.A, Bader J.S, Chandler D, Sprik M, Klein M, Impey R.W. Molecular model for aqueous ferrous-ferric electron transfer. J Chem Phys 1991;3627-3633.
-
(1991)
J Chem Phys
, pp. 3627-3633
-
-
Kuharsi, R.A.1
Bader, J.S.2
Chandler, D.3
Sprik, M.4
Klein, M.5
Impey, R.W.6
-
55
-
-
84961979623
-
Generalized Linear Response Approximation in Discrete Methods
-
Orozco M, Luque FJ. Generalized Linear Response Approximation in Discrete Methods. Chem Phys Lett 1997;265:473-480
-
(1997)
Chem Phys Lett
, vol.265
, pp. 473-480
-
-
Orozco, M.1
Luque, F.J.2
-
56
-
-
84962432699
-
Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes
-
Miertus S, Tomasi J. Approximate evaluations of the electrostatic free energy and internal energy changes in solution processes. Chem Phys 1982;65:239-245
-
(1982)
Chem Phys
, vol.65
, pp. 239-245
-
-
Miertus, S.1
Tomasi, J.2
-
57
-
-
84946893847
-
Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects
-
Miertus S, Scrocco E, Tomasi J. Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects. Chem Phys 1981;55:117-129
-
(1981)
Chem Phys
, vol.55
, pp. 117-129
-
-
Miertus, S.1
Scrocco, E.2
Tomasi, J.3
-
58
-
-
84986477837
-
Optimization of solute cavities and van der Waals parameters in ab initio MST-SCRF calculations of neutral molecules
-
Bachs M, Luque FJ, Orozco M. Optimization of solute cavities and van der Waals parameters in ab initio MST-SCRF calculations of neutral molecules. J Comput Chem 1994;15:446-454
-
(1994)
J Comput Chem
, vol.15
, pp. 446-454
-
-
Bachs, M.1
Luque, F.J.2
Orozco, M.3
-
59
-
-
84986518879
-
Development of optimized MST/ SCRF methods for semiempirical calculations: The MNDO and PM3 Hamiltonians
-
Orozco M, Bachs M, Luque FJ. Development of optimized MST/ SCRF methods for semiempirical calculations: the MNDO and PM3 Hamiltonians. J Comput Chem 1995;16:563-575
-
(1995)
J Comput Chem
, vol.16
, pp. 563-575
-
-
Orozco, M.1
Bachs, M.2
Luque, F.J.3
-
60
-
-
33748650102
-
Solvent Effects in Chloroform Solution: Parametrization of the MST/SCRF Continuum Model
-
Luque FJ, ZhangY, Aleman C, Bachs M, Gao J, Orozco M. Solvent Effects in Chloroform Solution: parametrization of the MST/SCRF Continuum Model. J Phys Chem 1996;100:4269-4276
-
(1996)
J Phys Chem
, vol.100
, pp. 4269-4276
-
-
Luque, F.J.1
Zhang, Y.2
Aleman, C.3
Bachs, M.4
Gao, J.5
Orozco, M.6
-
61
-
-
84962338805
-
Extension of MST/SCRF method to organic solvents: Ab initio and semiempirical parametrization for neutral solutes in CC14
-
Luque FJ, Alemán C, Bachs M, Orozco M. Extension of MST/SCRF method to organic solvents: ab initio and semiempirical parametrization for neutral solutes in CC14. J Comput Chem 1996;17:806-820
-
(1996)
J Comput Chem
, vol.17
, pp. 806-820
-
-
Luque, F.J.1
Alemán, C.2
Bachs, M.3
Orozco, M.4
-
62
-
-
84962363009
-
-
Insight II Computer Program Accelrys Co., San Diego, CA. 2003
-
Insight II Computer Program Accelrys Co., San Diego, CA. 2003
-
-
-
-
63
-
-
0035576327
-
Classical molecular interaction potentials: Improved setup procedure in molecular dynamics simulations of proteins
-
Gelpi JL, Kalko SG, Barril X, Cirera J, de la Cruz X, Luque FJ, Orozco M. Classical molecular interaction potentials: improved setup procedure in molecular dynamics simulations of proteins. Proteins 2001;45:428-437
-
(2001)
Proteins
, vol.45
, pp. 428-437
-
-
Gelpi, J.L.1
Kalko, S.G.2
Barril, X.3
Cirera, J.4
De La Cruz, X.5
Luque, F.J.6
Orozco, M.7
-
64
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. 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
-
65
-
-
33846823909
-
Particle mesh Ewald: An NXlog(N) method for Ewald sums in large systems
-
Darden TA, York DM, Pedersen LG. Particle mesh Ewald: an NXlog(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.A.1
York, D.M.2
Pedersen, L.G.3
-
66
-
-
0029011701
-
A second generation force field for the simulation of proteins nucleic acids and organic molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Fergurson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. 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
Fergurson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
67
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 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
-
68
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly CE, Cieplak P, Cornell WD, Kollman PA. 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.E.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
69
-
-
0004209777
-
-
University of California, San Francisco
-
Case DA, Pearlman DA, Caldwell JW, Cheatham TE III, Ross WS, Simmerling CL, Darden TL, Marz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA. AMBER6. University of California, San Francisco. 1999
-
(1999)
AMBER6
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.L.7
Marz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Tsui, V.13
Radmer, R.J.14
Duan, Y.15
Pitera, J.16
Massova, I.17
Seibel, G.L.18
Singh, U.C.19
Weiner, P.K.20
Kollman, P.A.21
more..
-
70
-
-
0029633186
-
AMBER a package of computer programs for applying molecular mechanics normal mode analysis molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, DeBolt S, Fergurson D, Seibel G, Kollman PA. AMBER a package of computer programs for applying molecular mechanics normal mode analysis molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules. Computer Physics Communications 1995;91:1-41
-
(1995)
Computer Physics Communications
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Fergurson, D.7
Seibel, G.8
Kollman, P.A.9
-
71
-
-
0000408363
-
Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO)
-
Weise J, Shenkin PS, Still WC. Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). J Comp Chem 1999;20:217-230
-
(1999)
J Comp Chem
, vol.20
, pp. 217-230
-
-
Weise, J.1
Shenkin, P.S.2
Still, W.C.3
-
72
-
-
0026612756
-
Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin
-
Bashford D, Gerwert K. Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin. J Mol Biol 1992;224:473-496
-
(1992)
J Mol Biol
, vol.224
, pp. 473-496
-
-
Bashford, D.1
Gerwert, K.2
-
73
-
-
0034701222
-
Molecular dynamics simulations of nucleic acids with a generalized born solvation model
-
Tsui V, Case D. Molecular dynamics simulations of nucleic acids with a generalized born solvation model. J Am Chem Soc 2000;122:2489-2498.
-
(2000)
J Am Chem Soc
, vol.122
, pp. 2489-2498
-
-
Tsui, V.1
Case, D.2
-
74
-
-
0346971105
-
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
-
Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL III. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. J Comput Chem 2004;25:265-284.
-
(2004)
J Comput Chem
, vol.25
, pp. 265-284
-
-
Feig, M.1
Onufriev, A.2
Lee, M.S.3
Im, W.4
Case, D.A.5
Brooks III, C.L.6
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