-
2
-
-
0035950796
-
Can absolute free energies of association be estimated from molecular mechanical simulations? the biotin-streptavidin system revisited
-
Dixit, S. B.; Chipot, C. Can absolute free energies of association be estimated from molecular mechanical simulations? The biotin-streptavidin system revisited J. Phys. Chem. A 2001, 105, 9795-9799
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 9795-9799
-
-
Dixit, S.B.1
Chipot, C.2
-
3
-
-
0141682863
-
Absolute binding free energies: A quantitative approach to their calculation
-
Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. Absolute binding free energies: A quantitative approach to their calculation J. Phys. Chem. B 2003, 107, 9535-9551
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 9535-9551
-
-
Boresch, S.1
Tettinger, F.2
Leitgeb, M.3
Karplus, M.4
-
4
-
-
7444257387
-
Efficient evaluation of binding free energy using continuum electrostatics solvation
-
Huang, D.; Caflisch, A. Efficient evaluation of binding free energy using continuum electrostatics solvation J. Med. Chem. 2004, 47, 5791-5797
-
(2004)
J. Med. Chem.
, vol.47
, pp. 5791-5797
-
-
Huang, D.1
Caflisch, A.2
-
5
-
-
18744372751
-
Calculation of absolute protein-ligand binding free energy from computer simulations
-
Woo, H. J.; Roux, B. Calculation of absolute protein-ligand binding free energy from computer simulations Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6825-6830
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 6825-6830
-
-
Woo, H.J.1
Roux, B.2
-
6
-
-
23744508332
-
Absolute free energy calculations by thermodynamic integration in four spatial dimensions
-
Rodinger, T.; Howell, P. L.; Pomès, R. Absolute free energy calculations by thermodynamic integration in four spatial dimensions J. Chem. Phys. 2005, 123, 34104
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 34104
-
-
Rodinger, T.1
Howell, P.L.2
Pomès, R.3
-
7
-
-
33749238080
-
Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant
-
Deng, Y.; Roux, B. Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant J. Chem. Theory Comput. 2006, 2, 1255-1273
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1255-1273
-
-
Deng, Y.1
Roux, B.2
-
8
-
-
34547648559
-
Simple estimation of absolute free energies for biomolecules
-
Ytreberg, F. M.; Zuckerman, D. M. Simple estimation of absolute free energies for biomolecules J. Chem. Phys. 2006, 124, 104105
-
(2006)
J. Chem. Phys.
, vol.124
, pp. 104105
-
-
Ytreberg, F.M.1
Zuckerman, D.M.2
-
9
-
-
33749532284
-
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials
-
Wang, J.; Deng, Y.; Roux, B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials Biophys. J. 2006, 91, 2798-2814
-
(2006)
Biophys. J.
, vol.91
, pp. 2798-2814
-
-
Wang, J.1
Deng, Y.2
Roux, B.3
-
10
-
-
34547110591
-
Predicting absolute ligand binding free energies to a simple model site
-
Mobley, D. L.; Graves, A. P.; Chodera, J. D.; McReynolds, A. C.; Shoichet, B. K.; Dill, K. A. Predicting absolute ligand binding free energies to a simple model site J. Mol. Biol. 2007, 371, 1118-1134
-
(2007)
J. Mol. Biol.
, vol.371
, pp. 1118-1134
-
-
Mobley, D.L.1
Graves, A.P.2
Chodera, J.D.3
McReynolds, A.C.4
Shoichet, B.K.5
Dill, K.A.6
-
11
-
-
44049091290
-
Calculation of protein-ligand binding free energy by using a polarizable potential
-
J., D.; Golubkov, P. A.; Darden, T. A.; Ren, P. Calculation of protein-ligand binding free energy by using a polarizable potential Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 6290-6295
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 6290-6295
-
-
Ju, D.1
Golubkov, P.A.2
Darden, T.A.3
Ren, P.4
-
12
-
-
54849417403
-
Calculation of absolute protein-ligand binding free energy using distributed replica sampling
-
Rodinger, T.; Howell, P. L.; Pomès, R. Calculation of absolute protein-ligand binding free energy using distributed replica sampling J. Chem. Phys. 2008, 129, 155102
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 155102
-
-
Rodinger, T.1
Howell, P.L.2
Pomès, R.3
-
13
-
-
65249124122
-
Computations of standard binding free energies with molecular dynamics simulations
-
Deng, Y.; Roux, B. Computations of standard binding free energies with molecular dynamics simulations J. Phys. Chem. B 2009, 113, 2234-2246
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 2234-2246
-
-
Deng, Y.1
Roux, B.2
-
14
-
-
70449522914
-
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
-
Boyce, S. E.; Mobley, D. L.; Rocklin, G. J.; Graves, A. P.; Dill, K. A.; Shoichet, B. K. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site J. Mol. Biol. 2009, 394, 747-763
-
(2009)
J. Mol. Biol.
, vol.394
, pp. 747-763
-
-
Boyce, S.E.1
Mobley, D.L.2
Rocklin, G.J.3
Graves, A.P.4
Dill, K.A.5
Shoichet, B.K.6
-
15
-
-
65249154272
-
Standard free energy of binding from a one-dimensional potential of mean force
-
Doudou, S.; Burton, N. A.; Henchman, R. H. Standard free energy of binding from a one-dimensional potential of mean force J. Chem. Theory Comput. 2009, 5, 909-918
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 909-918
-
-
Doudou, S.1
Burton, N.A.2
Henchman, R.H.3
-
16
-
-
77956574437
-
Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations
-
Jiang, W.; Roux, B. Free energy perturbation Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations J. Chem. Theory Comput. 2010, 6, 2559-2565
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2559-2565
-
-
Jiang, W.1
Roux, B.2
-
17
-
-
77951210462
-
Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions
-
Singh, N.; Warshel, A. Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions Proteins 2010, 78, 1705-1723
-
(2010)
Proteins
, vol.78
, pp. 1705-1723
-
-
Singh, N.1
Warshel, A.2
-
18
-
-
83455177830
-
Calculation of the absolute free energy of binding and related entropies with the HSMD-TI method: The FKBP12-L8 complex
-
General, I. J.; Dragomirova, R.; Meirovitch, H. Calculation of the absolute free energy of binding and related entropies with the HSMD-TI method: The FKBP12-L8 complex J. Chem. Theory Comput. 2011, 7, 4196-4207
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 4196-4207
-
-
General, I.J.1
Dragomirova, R.2
Meirovitch, H.3
-
19
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch, I.; Giorgino, T.; Fabritiis, G. D. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 10184-10189
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
Fabritiis, G.D.3
-
20
-
-
78651242089
-
New method for calculating the absolute free energy of binding: The effect of a mobile loop on the avidin/biotin complex
-
General, I. J.; Dragomirova, R.; Meirovitch, H. New method for calculating the absolute free energy of binding: The effect of a mobile loop on the avidin/biotin complex J. Phys. Chem. B 2011, 115, 168-175
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 168-175
-
-
General, I.J.1
Dragomirova, R.2
Meirovitch, H.3
-
21
-
-
84862271828
-
Absolute free energy of binding of avidin/biotin, revisited
-
General, I. J.; Dragomirova, R.; Meirovitch, H. Absolute free energy of binding of avidin/biotin, revisited J. Phys. Chem. B 2012, 116, 6628-6636
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 6628-6636
-
-
General, I.J.1
Dragomirova, R.2
Meirovitch, H.3
-
22
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
Kollman, P. A. Free energy calculations: Applications to chemical and biochemical phenomena Chem. Rev. 1993, 93, 2395-2417
-
(1993)
Chem. Rev.
, vol.93
, pp. 2395-2417
-
-
Kollman, P.A.1
-
23
-
-
0027239578
-
What determines the strength of noncovalent association of ligands to proteins in aqueous solution?
-
Miyamoto, S.; Kollman, P. A. What determines the strength of noncovalent association of ligands to proteins in aqueous solution? Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 8402-8406
-
(1993)
Proc. Natl. Acad. Sci. U.S.A.
, vol.90
, pp. 8402-8406
-
-
Miyamoto, S.1
Kollman, P.A.2
-
25
-
-
36849122972
-
High-temperature equation of state by a perturbation method. I. Nonpolar gases
-
Zwanzig, R. W. High-temperature equation of state by a perturbation method. I. Nonpolar gases J. Chem. Phys. 1954, 22, 1420-1426
-
(1954)
J. Chem. Phys.
, vol.22
, pp. 1420-1426
-
-
Zwanzig, R.W.1
-
26
-
-
80052001378
-
Pathway and mechanism of drug binding to G-protein-coupled receptors
-
Dror, R. O.; Pan, A. C.; Arlow, D. H.; Borhani, D. W.; Maragakis, P.; Shan, Y.; Xu, H.; Shaw, D. E. Pathway and mechanism of drug binding to G-protein-coupled receptors Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 13118-13123
-
(2011)
Proc. Natl. Acad. Sci. U.S.A.
, vol.108
, pp. 13118-13123
-
-
Dror, R.O.1
Pan, A.C.2
Arlow, D.H.3
Borhani, D.W.4
Maragakis, P.5
Shan, Y.6
Xu, H.7
Shaw, D.E.8
-
27
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The statistical-thermodynamic basis for computation of binding affinities: A critical review Biophys. J. 1997, 72, 1047-1069
-
(1997)
Biophys. J.
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
28
-
-
0030887944
-
Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
-
Hermans, J.; Wang, L. Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme J. Am. Chem. Soc. 1997, 119, 2707-2714
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 2707-2714
-
-
Hermans, J.1
Wang, L.2
-
29
-
-
0009590921
-
Free-energy calculations: A breakthrough for modeling organic chemistry in solutions
-
Jorgensen, W. L. Free-energy calculations: A breakthrough for modeling organic chemistry in solutions Acc. Chem. Res. 1989, 22, 184-189
-
(1989)
Acc. Chem. Res.
, vol.22
, pp. 184-189
-
-
Jorgensen, W.L.1
-
30
-
-
85005687495
-
The free energy of xenon binding to myoglobin from molecular dynamics simulation
-
Hermans, J.; Shankar, S. The free energy of xenon binding to myoglobin from molecular dynamics simulation Isr. J. Chem. 1986, 27, 225-227
-
(1986)
Isr. J. Chem.
, vol.27
, pp. 225-227
-
-
Hermans, J.1
Shankar, S.2
-
31
-
-
0029757992
-
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study
-
Roux, B.; Nina, M.; Pomès, R.; Smith, J. C. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: A molecular dynamics free energy perturbation study Biophys. J. 1996, 71, 670-681
-
(1996)
Biophys. J.
, vol.71
, pp. 670-681
-
-
Roux, B.1
Nina, M.2
Pomès, R.3
Smith, J.C.4
-
32
-
-
33646415982
-
Direct calculation of the binding free energies of FKBP ligands
-
Fujitani, H.; Tanida, Y.; Ito, M.; Jayachandran, G.; Snow, C. D.; Shirts, M. R.; Sorin, E. J.; Pande, V. S. Direct calculation of the binding free energies of FKBP ligands J. Chem. Phys. 2005, 123, 084108
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 084108
-
-
Fujitani, H.1
Tanida, Y.2
Ito, M.3
Jayachandran, G.4
Snow, C.D.5
Shirts, M.R.6
Sorin, E.J.7
Pande, V.S.8
-
33
-
-
21544442740
-
Computer-simulation study of free-energy barriers in crystal nucleation
-
van Duijneveldt, S.; Frenkel, D. Computer-simulation study of free-energy barriers in crystal nucleation J. Chem. Phys. 1992, 96, 4655-4668
-
(1992)
J. Chem. Phys.
, vol.96
, pp. 4655-4668
-
-
Van Duijneveldt, S.1
Frenkel, D.2
-
34
-
-
0346350789
-
The development of replica-exchange-based free-energy methods
-
Woods, C. J.; Essex, J. W.; King, M. A. The development of replica-exchange-based free-energy methods J. Phys. Chem. B 2003, 107, 13703-13710
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 13703-13710
-
-
Woods, C.J.1
Essex, J.W.2
King, M.A.3
-
35
-
-
0001167023
-
Interactions between amides in solution and the thermodynamics of weak binding
-
Jorgensen, W. L. Interactions between amides in solution and the thermodynamics of weak binding J. Am. Chem. Soc. 1989, 111, 3770-3771
-
(1989)
J. Am. Chem. Soc.
, vol.111
, pp. 3770-3771
-
-
Jorgensen, W.L.1
-
36
-
-
0030987036
-
Molecular dynamics study of unbinding of the avidin-biotin complex
-
Izrailev, S.; Stepaniants, S.; Balsera, M.; Oono, Y.; Schulten, K. Molecular dynamics study of unbinding of the avidin-biotin complex Biophys. J. 1997, 72, 1568-1581
-
(1997)
Biophys. J.
, vol.72
, pp. 1568-1581
-
-
Izrailev, S.1
Stepaniants, S.2
Balsera, M.3
Oono, Y.4
Schulten, K.5
-
37
-
-
0036312338
-
Early mechanistic events in biotin dissociation from streptavidin
-
Hyre, D. E.; Amon, L. M.; E.Penzotti, J.; Trong, I. L.; Stenkamp, R. E.; Lybrand, T. P.; Stayton, P. S. Early mechanistic events in biotin dissociation from streptavidin Nat. Struct. Biol. 2002, 9, 582-585
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 582-585
-
-
Hyre, D.E.1
Amon, L.M.2
Penzotti, J.E.3
Trong, I.L.4
Stenkamp, R.E.5
Lybrand, T.P.6
Stayton, P.S.7
-
38
-
-
0347089020
-
Energetics of ion conduction through the gramicidin channel
-
Allen, T.; Andersen, O.; Roux, B. Energetics of ion conduction through the gramicidin channel Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 117-122
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 117-122
-
-
Allen, T.1
Andersen, O.2
Roux, B.3
-
39
-
-
33646178918
-
Calculation of absolute protein-ligand binding affinity using path and endpoint approaches
-
Lee, M. S.; Olson, M. A. Calculation of absolute protein-ligand binding affinity using path and endpoint approaches Biophys. J. 2006, 90, 864-877
-
(2006)
Biophys. J.
, vol.90
, pp. 864-877
-
-
Lee, M.S.1
Olson, M.A.2
-
40
-
-
0020199402
-
Role of diffusion in ligand binding to macromolecules and cell-bound receptors
-
Shoup, D.; Szabo, A. Role of diffusion in ligand binding to macromolecules and cell-bound receptors Biophys. J. 1982, 40, 33-39
-
(1982)
Biophys. J.
, vol.40
, pp. 33-39
-
-
Shoup, D.1
Szabo, A.2
-
41
-
-
78751690788
-
Dual role of protein phosphorylation in DNA activator/coactivator binding
-
Dadarlat, V. M.; Skeel, R. D. Dual role of protein phosphorylation in DNA activator/coactivator binding Biophys. J. 2011, 100, 469-477
-
(2011)
Biophys. J.
, vol.100
, pp. 469-477
-
-
Dadarlat, V.M.1
Skeel, R.D.2
-
42
-
-
84861375893
-
End-to-end attraction of duplex DNA
-
Maffeo, C.; Luan, B.; Aksimentiev, A. End-to-end attraction of duplex DNA Nucleic Acids Res. 2012, 40, 3812-3821
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 3812-3821
-
-
Maffeo, C.1
Luan, B.2
Aksimentiev, A.3
-
43
-
-
0029782121
-
Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain
-
Pisabarro, M. T.; Serrano, L. Rational design of specific high-affinity peptide ligands for the Abl-SH3 domain Biochemistry 1996, 35, 10634-10640
-
(1996)
Biochemistry
, vol.35
, pp. 10634-10640
-
-
Pisabarro, M.T.1
Serrano, L.2
-
44
-
-
0032555743
-
Crystal structure of the Abl-SH3 domain complexed with a designed high-affinity peptide ligand: Implications for SH3-ligand interactions
-
Pisabarro, M. T.; Serrano, L.; Wilmanns, M. Crystal structure of the Abl-SH3 domain complexed with a designed high-affinity peptide ligand: Implications for SH3-ligand interactions J. Mol. Biol. 1998, 281, 513-521
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 513-521
-
-
Pisabarro, M.T.1
Serrano, L.2
Wilmanns, M.3
-
45
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
-
Torrie, G. M.; Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling J. Comput. Phys. 1977, 23, 187-199
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
46
-
-
0029633155
-
The calculation of the potential of mean force using computer simulations
-
Roux, B. The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 1995, 91, 275-282
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 275-282
-
-
Roux, B.1
-
47
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding Chem. Phys. Lett. 1999, 314, 141-151
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
48
-
-
0034294024
-
Multidimensional replica-exchange method for free-energy calculations
-
Sugita, Y.; Kitao, A.; Okamoto, Y. Multidimensional replica-exchange method for free-energy calculations J. Chem. Phys. 2000, 113, 6042-6051
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
49
-
-
0035935802
-
Calculating free energies using average force
-
Darve, E.; Pohorille, A. Calculating free energies using average force J. Chem. Phys. 2001, 115, 9169-9183
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 9169-9183
-
-
Darve, E.1
Pohorille, A.2
-
50
-
-
4344660645
-
Overcoming free energy barriers using unconstrained molecular dynamics simulations
-
Hénin, J.; Chipot, C. Overcoming free energy barriers using unconstrained molecular dynamics simulations J. Chem. Phys. 2004, 121, 2904-2914
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 2904-2914
-
-
Hénin, J.1
Chipot, C.2
-
51
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C. 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 Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-Mccarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
-
52
-
-
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., Jr.; Feig, M.; Brooks, C. L., III 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 Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
53
-
-
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
-
54
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, L.; Kalé, R. D.; Schulten, K. Scalable molecular dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, L.8
Kalé, R.D.9
Schulten, K.10
-
55
-
-
36449007836
-
Constant pressure molecular dynamics simulations - The Langevin piston method
-
Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. Constant pressure molecular dynamics simulations-The Langevin piston method J. Chem. Phys. 1995, 103, 4613-4621
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4613-4621
-
-
Feller, S.E.1
Zhang, Y.H.2
Pastor, R.W.3
Brooks, B.R.4
-
56
-
-
33846823909
-
Particle mesh Ewald: An N log N method for ewald sums in large systems
-
Darden, T. A.; York, D. M.; Pedersen, L. G. Particle mesh Ewald: An N log N method for ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.A.1
York, D.M.2
Pedersen, L.G.3
-
57
-
-
33646650705
-
Reversible multiple time scale molecular dynamics
-
Tuckerman, M. E.; Berne, B. J.; Martyna, G. J. Reversible multiple time scale molecular dynamics J. Phys. Chem. B 1992, 97, 1990-2001
-
(1992)
J. Phys. Chem. B
, vol.97
, pp. 1990-2001
-
-
Tuckerman, M.E.1
Berne, B.J.2
Martyna, G.J.3
-
58
-
-
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
-
59
-
-
36449002336
-
Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration
-
Zacharias, M.; Straatsma, T. P.; McCammon, J. A. Separation-shifted scaling, a new scaling method for Lennard-Jones interactions in thermodynamic integration J. Chem. Phys. 1994, 100, 9025-9031
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9025-9031
-
-
Zacharias, M.1
Straatsma, T.P.2
McCammon, J.A.3
-
60
-
-
5244304444
-
Efficient estimation of free energy differences from Monte Carlo data
-
Bennett, C. H. Efficient estimation of free energy differences from Monte Carlo data J. Chem. Phys. 1976, 22, 245-268
-
(1976)
J. Chem. Phys.
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
61
-
-
52949088587
-
Statistically optimal analysis of samples from multiple equilibrium states
-
Shirts, M. R.; Chodera, J. D. Statistically optimal analysis of samples from multiple equilibrium states J. Chem. Phys. 2008, 129, 124105
-
(2008)
J. Chem. Phys.
, vol.129
, pp. 124105
-
-
Shirts, M.R.1
Chodera, J.D.2
-
62
-
-
77950102787
-
Exploring multidimensional free energy landscapes using time-dependent biases on collective variables
-
Hénin, J.; Forin, G.; Chipot, C.; Klein, M. L. Exploring multidimensional free energy landscapes using time-dependent biases on collective variables J. Chem. Theory Comput. 2010, 6, 35-47
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 35-47
-
-
Hénin, J.1
Forin, G.2
Chipot, C.3
Klein, M.L.4
-
63
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method J. Comput. Chem. 1992, 13, 1011-1021
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
64
-
-
77949631889
-
-
version 2.0.6; Grossfield Lab: Rochester, NY
-
Grossfield, A. WHAM: the Weighted Histogram Analysis Method, version 2.0.6; Grossfield Lab: Rochester, NY, 2012. Available online: http://membrane.urmc.rochester.edu/content/wham.
-
(2012)
WHAM: The Weighted Histogram Analysis Method
-
-
Grossfield, A.1
-
65
-
-
84855688941
-
Convergence and error estimation in free energy calculations using the weighted histogram analysis method
-
Zhu, F.; Hummer, G. Convergence and error estimation in free energy calculations using the weighted histogram analysis method J. Comput. Chem. 2012, 33, 453-465
-
(2012)
J. Comput. Chem.
, vol.33
, pp. 453-465
-
-
Zhu, F.1
Hummer, G.2
-
66
-
-
0034870959
-
Contribution of translational and rotational motions to molecular association in aqueous solution
-
Yu, Y. B.; Privalov, P. L.; Hodges, R. S. Contribution of translational and rotational motions to molecular association in aqueous solution Biophys. J. 2001, 81, 1632-1642
-
(2001)
Biophys. J.
, vol.81
, pp. 1632-1642
-
-
Yu, Y.B.1
Privalov, P.L.2
Hodges, R.S.3
-
67
-
-
58149512801
-
Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems
-
Zheng, L.; Chen, M.; Yang, W. Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems Proc. Natl. Acad. Sci. U.S.A. 2008, 51, 20227-20232
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.51
, pp. 20227-20232
-
-
Zheng, L.1
Chen, M.2
Yang, W.3
-
68
-
-
4243661501
-
Constrained reaction coordinate dynamics for the simulation of rare events
-
Carter, E. A.; Ciccotti, G.; Hynes, J. T.; Kapral, R. Constrained reaction coordinate dynamics for the simulation of rare events Chem. Phys. Lett. 1989, 156, 472-477
-
(1989)
Chem. Phys. Lett.
, vol.156
, pp. 472-477
-
-
Carter, E.A.1
Ciccotti, G.2
Hynes, J.T.3
Kapral, R.4
-
69
-
-
38849144001
-
Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method
-
Khavrutskii, I. V.; Dzubiella, J.; McCammon, J. A. Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method J. Chem. Phys. 2008, 128, 044106
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 044106
-
-
Khavrutskii, I.V.1
Dzubiella, J.2
McCammon, J.A.3
-
70
-
-
77955577540
-
Good practices in free-energy calculations
-
Pohorille, A.; Jarzynski, C.; Chipot, C. Good practices in free-energy calculations J. Phys. Chem. B 2010, 114, 10235-10253
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 10235-10253
-
-
Pohorille, A.1
Jarzynski, C.2
Chipot, C.3
-
71
-
-
33645776269
-
Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain
-
Hou, T.; Chen, K.; McLaughlin, W. A.; Lu, B.; Wang, W. Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain PLoS Comput. Biol. 2006, 2, 0046-0055
-
(2006)
PLoS Comput. Biol.
, vol.2
, pp. 0046-0055
-
-
Hou, T.1
Chen, K.2
McLaughlin, W.A.3
Lu, B.4
Wang, W.5
-
72
-
-
0004504539
-
Monte Carlo simulation of differences in free energies of hydration
-
Jorgensen, W.; Ravimohan, C. Monte Carlo simulation of differences in free energies of hydration J. Chem. Phys. 1985, 83, 3050-3054
-
(1985)
J. Chem. Phys.
, vol.83
, pp. 3050-3054
-
-
Jorgensen, W.1
Ravimohan, C.2
-
73
-
-
33746255471
-
String method in collective variables: Minimum free energy paths and isocommittor surfaces
-
Maragliano, L.; Fischer, A.; Vanden-Eijnden, E.; Ciccotti, G. String method in collective variables: Minimum free energy paths and isocommittor surfaces J. Chem. Phys. 2006, 125, 024106
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 024106
-
-
Maragliano, L.1
Fischer, A.2
Vanden-Eijnden, E.3
Ciccotti, G.4
-
74
-
-
61449194210
-
Binding specificity of SH2 domains: Insight from free energy simulations
-
Gan, W.; Roux, B. Binding specificity of SH2 domains: insight from free energy simulations Proteins: Struct., Func., Bioinf. 2009, 74, 996-1007
-
(2009)
Proteins: Struct., Func., Bioinf.
, vol.74
, pp. 996-1007
-
-
Gan, W.1
Roux, B.2
-
75
-
-
84865723813
-
2 dihedral angles
-
2 dihedral angles J. Chem. Theory Comput. 2012, 8, 3257-3273
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3257-3273
-
-
Best, R.B.1
Zhu, X.2
Shim, J.3
Lopes, P.E.4
Mittal, J.5
Feig, M.6
Mackerell Jr., A.D.7
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