-
1
-
-
36749107785
-
Molecular dynamics simulations at constant pressure and/or temperature
-
Andersen, H. C. 1980. Molecular dynamics simulations at constant pressure and/or temperature. J. Chem. Phys. 72:2384-2393.
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 2384-2393
-
-
Andersen, H.C.1
-
2
-
-
48749148224
-
RATTLE: A "velocity" version of the SHAKE algorithm for molecular dynamics
-
Andersen, H. C. 1983. RATTLE: a "velocity" version of the SHAKE algorithm for molecular dynamics. J. Comput. Phys. 52:24-34.
-
(1983)
J. Comput. Phys.
, vol.52
, pp. 24-34
-
-
Andersen, H.C.1
-
3
-
-
0003039369
-
Molecular dynamics and transition state theory: The simulation of infrequent events
-
R. Christofferson, editor. ACS Symposium Series No. 46, American Chemical Society, Washington, DC
-
Bennett, C. H. 1977. Molecular dynamics and transition state theory: the simulation of infrequent events. In Algorithms for Chemical Computations. R. Christofferson, editor. ACS Symposium Series No. 46, American Chemical Society, Washington, DC. 63-97.
-
(1977)
Algorithms for Chemical Computations
, pp. 63-97
-
-
Bennett, C.H.1
-
4
-
-
0029070488
-
Folding of protein-G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements
-
Blanco, F. J., and L. Serrano. 1995. Folding of protein-G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur. J. Biochem. 230:634-649.
-
(1995)
Eur. J. Biochem.
, vol.230
, pp. 634-649
-
-
Blanco, F.J.1
Serrano, L.2
-
5
-
-
0028500779
-
A short linear peptide that folds into a native stable β-hairpin in aqueous-solution
-
Blanco, F. J., G. Rivas, and L. Serrano. 1994. A short linear peptide that folds into a native stable β-hairpin in aqueous-solution. Nat. Struct. Biol. 1:584-590.
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 584-590
-
-
Blanco, F.J.1
Rivas, G.2
Serrano, L.3
-
6
-
-
0142027789
-
Transition-path sampling of β-hairpin folding
-
Bolhuis, P. G. 2003a. Transition-path sampling of β-hairpin folding. Proc. Natl. Acad. Sci. USA. 100:12129-12134.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12129-12134
-
-
Bolhuis, P.G.1
-
7
-
-
0037439656
-
Transition path sampling on diffusive barriers
-
Bolhuis, P. G. 2003b. Transition path sampling on diffusive barriers. J. Phys. Condens. Matter. 15:5113-5120.
-
(2003)
J. Phys. Condens. Matter.
, vol.15
, pp. 5113-5120
-
-
Bolhuis, P.G.1
-
8
-
-
0034321137
-
Transition path sampling of cavitation between molecular scale solvophobic surfaces
-
Bolhuis, P. G., and D. Chandler. 2000. Transition path sampling of cavitation between molecular scale solvophobic surfaces. J. Chem. Phys. 113:8154-8160.
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 8154-8160
-
-
Bolhuis, P.G.1
Chandler, D.2
-
9
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
Bolhuis, P. G., D. Chandler, C. Dellago, and P. Geissler. 2002. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 54:291-318.
-
(2002)
Annu. Rev. Phys. Chem.
, vol.54
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.4
-
10
-
-
2742515916
-
Sampling ensembles of deterministic transition pathways
-
Bolhuis, P. G., C. Dellago, and D. Chandler. 1998. Sampling ensembles of deterministic transition pathways. Faraday Discuss. 110:421-436.
-
(1998)
Faraday Discuss.
, vol.110
, pp. 421-436
-
-
Bolhuis, P.G.1
Dellago, C.2
Chandler, D.3
-
12
-
-
33748374124
-
Statistical mechanics of isomerization dynamics in liquids and the transition state
-
Chandler, D. 1978. Statistical mechanics of isomerization dynamics in liquids and the transition state. J. Chem. Phys. 68:2959-2970.
-
(1978)
J. Chem. Phys.
, vol.68
, pp. 2959-2970
-
-
Chandler, D.1
-
13
-
-
0037154268
-
Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
-
Cheung, M. S., A. E. García, and J. N. Onuchic. 2003. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc. Natl. Acad. Sci. USA. 99:685-690.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 685-690
-
-
Cheung, M.S.1
García, A.E.2
Onuchic, J.N.3
-
14
-
-
0000801009
-
Efficient transition path sampling: Application to Lennard-Jones cluster rearrangement
-
Dellago, C., P. G. Bolhuis, and D. Chandler. 1998a. Efficient transition path sampling: application to Lennard-Jones cluster rearrangement. J. Chem. Phys. 108:9236-9245.
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 9236-9245
-
-
Dellago, C.1
Bolhuis, P.G.2
Chandler, D.3
-
15
-
-
0000729781
-
Transition path sampling and the calculation of rate constants
-
Dellago, C., P. G. Bolhuis, F. S. Csajka, and D. Chandler. 1998b. Transition path sampling and the calculation of rate constants. J. Chem. Phys. 108:1964-1977.
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 1964-1977
-
-
Dellago, C.1
Bolhuis, P.G.2
Csajka, F.S.3
Chandler, D.4
-
16
-
-
4444242987
-
On the calculation of reaction rate constants in the transition path ensemble
-
Dellago, C., P. G. Bolhuis, and D. Chandler. 1999. On the calculation of reaction rate constants in the transition path ensemble. J. Chem. Phys. 110:6617-6625.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 6617-6625
-
-
Dellago, C.1
Bolhuis, P.G.2
Chandler, D.3
-
19
-
-
0035250027
-
Simulation of protein folding by reaction path annealing
-
Eastman, P., N. Grønbech-Jensen, and S. Doniach. 2001. Simulation of protein folding by reaction path annealing. J. Chem. Phys. 114:3823-3841.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 3823-3841
-
-
Eastman, P.1
Grønbech-Jensen, N.2
Doniach, S.3
-
20
-
-
0345133287
-
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
-
García, A. E., and J. N. Onuchic. 2003. Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc. Natl. Acad. Sci. USA. 100:13898-13904.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13898-13904
-
-
García, A.E.1
Onuchic, J.N.2
-
21
-
-
0035865992
-
Exploring the energy landscape of a β-hairpin in explicit solvent
-
García, A. E., and K. Y. Sanbonmatsu. 2001. Exploring the energy landscape of a β-hairpin in explicit solvent. Proteins Struct. Funct. Gen. 42:345-354.
-
(2001)
Proteins Struct. Funct. Gen.
, vol.42
, pp. 345-354
-
-
García, A.E.1
Sanbonmatsu, K.Y.2
-
22
-
-
0344270866
-
Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA
-
Hagan. M. F., A. R. Dinner, D. Chandler, and A. K. Chakraborty. 2003. Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA. Proc. Natl. Acad. Sci. USA. 100:13922-13927.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13922-13927
-
-
Hagan, M.F.1
Dinner, A.R.2
Chandler, D.3
Chakraborty, A.K.4
-
23
-
-
0034645735
-
Thermodynamics of a β-hairpin structure: Evidence for cooperative formation of folding nucleus
-
Honda, S., N. Kobayashi, and E. Munekata. 2000. Thermodynamics of a β-hairpin structure: evidence for cooperative formation of folding nucleus. J. Mol. Biol. 295:269-278.
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 269-278
-
-
Honda, S.1
Kobayashi, N.2
Munekata, E.3
-
25
-
-
0042415783
-
Greater scalability for parallel molecular dynamics
-
Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. 1999. Greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
26
-
-
0034646218
-
Mechanisms and kinetics of β-hairpin formation
-
Klimov, D. K., and D. Thirumalai. 2000. Mechanisms and kinetics of β-hairpin formation. Proc. Natl. Acad. Sci. USA. 97:2544-2549.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 2544-2549
-
-
Klimov, D.K.1
Thirumalai, D.2
-
27
-
-
0032764074
-
Dynamics and thermodynamics of β-hairpin assembly: Insights from various simulation techniques
-
Kolinski, A., B. Ilkowski, and J. Skolnick. 1999. Dynamics and thermodynamics of β-hairpin assembly: insights from various simulation techniques. Biophys. J. 77:2942-2952.
-
(1999)
Biophys. J.
, vol.77
, pp. 2942-2952
-
-
Kolinski, A.1
Ilkowski, B.2
Skolnick, J.3
-
28
-
-
0034598946
-
Molecular dynamics simulations of a β-hairpin fragment of protein-G: Balance between side-chain and backbone forces
-
Ma, B., and R. Nussinov. 2000. Molecular dynamics simulations of a β-hairpin fragment of protein-G: balance between side-chain and backbone forces. J. Mol. Biol. 296:1091-1104.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1091-1104
-
-
Ma, B.1
Nussinov, R.2
-
29
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, M. J. Field, J. Fischer, S. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stole, J. Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 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, J.7
Gao, S.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
Michnick, S.16
Ngo, T.17
Nguyen, D.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stole, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
30
-
-
1842581318
-
Rate constants for diffusive processes by partial path sampling
-
Moroni, D., T. van A., and P. G. Bolhuis. 2004. Rate constants for diffusive processes by partial path sampling. J. Chem. Phys. 120:4055-4065.
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 4055-4065
-
-
Moroni, D.1
Van, A.T.2
Bolhuis, P.G.3
-
31
-
-
0032568537
-
A statistical mechanical model for β-hairpin kinetics
-
Muñoz, V., E. R. Henry, J. Hofrichter, and W. A. Eaton. 1998. A statistical mechanical model for β-hairpin kinetics. Proc. Natl. Acad. Sci. USA. 95:5872-5879.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 5872-5879
-
-
Muñoz, V.1
Henry, E.R.2
Hofrichter, J.3
Eaton, W.A.4
-
32
-
-
0038502170
-
Folding dynamics and mechanism of β-hairpin formation
-
Muñoz, V., P. A. Thomson, J. Hofrichter, and W. A. Eaton. 1997. Folding dynamics and mechanism of β-hairpin formation. Nature. 390:196-199.
-
(1997)
Nature
, vol.390
, pp. 196-199
-
-
Muñoz, V.1
Thomson, P.A.2
Hofrichter, J.3
Eaton, W.A.4
-
33
-
-
0344702698
-
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
-
Nymeyer, H., and A. E. García. 2003. Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc. Natl. Acad. Sci. USA. 100:13934-13939.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13934-13939
-
-
Nymeyer, H.1
García, A.E.2
-
34
-
-
0033529908
-
Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein-G
-
Pande, V. S., and D. S. Rokhsar. 1999. Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein-G. Proc. Natl. Acad. Sci. USA. 96:9062-9067.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 9062-9067
-
-
Pande, V.S.1
Rokhsar, D.S.2
-
35
-
-
0032881707
-
A molecular dynamics study of the 41-56 β-hairpin from B1 domain of protein-G
-
Roccatano, D., A. Amadel, A. Di Nola, and H. J. C. Berendsen. 1999. A molecular dynamics study of the 41-56 β-hairpin from B1 domain of protein-G. Protein Sci. 8:2130-2143.
-
(1999)
Protein Sci.
, vol.8
, pp. 2130-2143
-
-
Roccatano, D.1
Amadel, A.2
Di Nola, A.3
Berendsen, H.J.C.4
-
36
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea, J.-E., and C. L. Brooks. 2001. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem. 52:499-535.
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 499-535
-
-
Shea, J.-E.1
Brooks, C.L.2
-
37
-
-
0032080053
-
Calculations on folding of segment B1 of streptococcal protein-G
-
Sheinerman, F. B., and C. L. Brooks. 1998a. Calculations on folding of segment B1 of streptococcal protein-G. J. Mol. Biol. 278:439-455.
-
(1998)
J. Mol. Biol.
, vol.278
, pp. 439-455
-
-
Sheinerman, F.B.1
Brooks, C.L.2
-
38
-
-
0032539561
-
Molecular picture of folding of a small α/β-protein
-
Sheinerman, F. B., and C. L. Brooks. 1998b. Molecular picture of folding of a small α/β-protein. Proc. Natl. Acad. Sci. USA. 95:1562-1567.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 1562-1567
-
-
Sheinerman, F.B.1
Brooks, C.L.2
-
39
-
-
0036217783
-
Long time dynamics of Met-enkephalin: Comparison of explicit and implicit solvent models
-
Shen, M., and K. F. Freed. 2002. Long time dynamics of Met-enkephalin: comparison of explicit and implicit solvent models. Biophys. J. 82:1791-1808.
-
(2002)
Biophys. J.
, vol.82
, pp. 1791-1808
-
-
Shen, M.1
Freed, K.F.2
-
40
-
-
3142707288
-
Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper β-hairpin
-
Singhal, N., C. Snow, and V. S. Pande. 2004. Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper β-hairpin. J. Chem. Phys. 121:415-425.
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 415-425
-
-
Singhal, N.1
Snow, C.2
Pande, V.S.3
-
42
-
-
0037059017
-
Evidence of turn and salt bridge contributions to β-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein-G
-
Tsai, J., and M. Levitt. 2002. Evidence of turn and salt bridge contributions to β-hairpin stability: MD simulations of C-terminal fragment from the B1 domain of protein-G. Biophys. Chem. 101:187-201.
-
(2002)
Biophys. Chem.
, vol.101
, pp. 187-201
-
-
Tsai, J.1
Levitt, M.2
-
43
-
-
0038515443
-
A novel path sampling method for the calculation of rate constants
-
van Erp, T., D. Moroni, and P. G. Bolhuis. 2003. A novel path sampling method for the calculation of rate constants. J. Chem. Phys. 118:7762-7774.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 7762-7774
-
-
Van Erp, T.1
Moroni, D.2
Bolhuis, P.G.3
-
44
-
-
0035850758
-
β-hairpin folding simulations in atomistic detail using an implicit solvent model
-
Zagrovic, B., E. J. Sorin, and V. S. Pande. 2001. β-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313:151-169.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 151-169
-
-
Zagrovic, B.1
Sorin, E.J.2
Pande, V.S.3
-
45
-
-
0036789950
-
Free energy landscape of a β-hairpin folding in water: Explicit vs. implicit solvent
-
Zhou, R., and B. J. Berne. 2002. Free energy landscape of a β-hairpin folding in water: explicit vs. implicit solvent. Proc. Natl. Acad. Sci. USA. 99:12777-12782.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12777-12782
-
-
Zhou, R.1
Berne, B.J.2
-
46
-
-
0035909921
-
The free energy landscape for β-hairpin folding in explicit water
-
Zhou, R., B. J. Berne, and R. Germain. 2001. The free energy landscape for β-hairpin folding in explicit water. Proc. Natl. Acad. Sci. USA. 98:14931-14936.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 14931-14936
-
-
Zhou, R.1
Berne, B.J.2
Germain, R.3
|