-
1
-
-
48749148224
-
Rattle: A "velocity" version of the Shake algorithm for molecular dynamics calculations
-
Andersen, H. C. 1983. Rattle: a "velocity" version of the Shake algorithm for molecular dynamics calculations. J. Comp. Phys. 52:24-34.
-
(1983)
J. Comp. Phys.
, vol.52
, pp. 24-34
-
-
Andersen, H.C.1
-
2
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein Data Bank. Nucleic Acids Res. 28:235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
5
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan, Y., and P. A. Kollman. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science. 282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
6
-
-
0034718553
-
Folding simulations of a three-stranded antiparallel β-sheet peptide
-
Ferrara, P., and A. Caflisch. 2000. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl. Acad. Sci. USA. 97:10780-10785.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
7
-
-
0037154980
-
Protein folding and unfolding at atomic resolution
-
Fersht, A. R., and V. Daggett. 2002. Protein folding and unfolding at atomic resolution. Cell. 108:573-582.
-
(2002)
Cell
, vol.108
, pp. 573-582
-
-
Fersht, A.R.1
Daggett, V.2
-
8
-
-
0345133287
-
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
-
Garcia, 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. 100:13898-13903.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13898-13903
-
-
Garcia, A.E.1
Onuchic, J.N.2
-
9
-
-
0035865992
-
Exploring the energy landscape of a beta hairpin in explicit solvent
-
Garcia, A. E., and K. Y. Sanbonmatsu. 2001. Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins. 42:345-354.
-
(2001)
Proteins
, vol.42
, pp. 345-354
-
-
Garcia, A.E.1
Sanbonmatsu, K.Y.2
-
10
-
-
33645941402
-
The OPLS potential functions for proteins: Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen, W. L., and J. Tirado-Rives. 1988. The OPLS potential functions for proteins: energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1666-1671.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1666-1671
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
11
-
-
0038054301
-
Experimental tests of villin subdomain folding simulations
-
Kubelka, J., W. A. Eaton, and J. Hofrichter. 2003. Experimental tests of villin subdomain folding simulations. J. Mol. Biol. 329:625-630.
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 625-630
-
-
Kubelka, J.1
Eaton, W.A.2
Hofrichter, J.3
-
12
-
-
0034610360
-
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
-
Mayor, U., C. M. Johnson, V. Daggett, and A. R. Fersht. 2000. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. USA. 97:13518-13522.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 13518-13522
-
-
Mayor, U.1
Johnson, C.M.2
Daggett, V.3
Fersht, A.R.4
-
13
-
-
0031058410
-
NMR structure of the 35-residue villin headpiece subdomain
-
McKnight, C. J., P. T. Matsudaira, and P. S. Kim. 1997. NMR structure of the 35-residue villin headpiece subdomain. Nat. Struct. Biol. 4:180-184.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 180-184
-
-
McKnight, C.J.1
Matsudaira, P.T.2
Kim, P.S.3
-
14
-
-
0036401140
-
Toward a taxonomy of the denatured state: Small angle scattering studies of unfolded proteins
-
Millett, I. S., S. Doniach, and K. W. Plaxco. 2002. Toward a taxonomy of the denatured state: small angle scattering studies of unfolded proteins. Adv. Protein Chem. 62:241-262.
-
(2002)
Adv. Protein Chem.
, vol.62
, pp. 241-262
-
-
Millett, I.S.1
Doniach, S.2
Plaxco, K.W.3
-
15
-
-
0037478676
-
Analysis of the distributed computing approach applied to the folding of a small beta peptide
-
Paci, E., A. Cavalli, M. Vendruscolo, and A. Caflisch. 2003. Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proc. Natl. Acad. Sci. USA. 100:8217-8222.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 8217-8222
-
-
Paci, E.1
Cavalli, A.2
Vendruscolo, M.3
Caflisch, A.4
-
16
-
-
0037235952
-
Atomistic protein folding simulations on the hundreds of microsecond timescale using worldwide distributed computing
-
Pande, V. S., I. Baker, J. Chapman, S. Elmer, S. Khaliq, S. Larson, Y. M. Rhee, M. R. Shirts, C. Snow, E. J. Sorin, and B. Zagrovic. 2002. Atomistic protein folding simulations on the hundreds of microsecond timescale using worldwide distributed computing. Biopolymers. 68:91-109.
-
(2002)
Biopolymers
, vol.68
, pp. 91-109
-
-
Pande, V.S.1
Baker, I.2
Chapman, J.3
Elmer, S.4
Khaliq, S.5
Larson, S.6
Rhee, Y.M.7
Shirts, M.R.8
Snow, C.9
Sorin, E.J.10
Zagrovic, B.11
-
17
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu, D., P. S. Shenkin, F. P. Hollinger, and W. C. Still. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. 101:3005-3014.
-
(1997)
J. Phys. Chem.
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
18
-
-
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, III. 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 III, C.L.2
-
19
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling, C., B. Strockbine, and A. E. Roitberg. 2002. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124:11258-11259.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
20
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow, C. D., H. Nguyen, V. S. Pande, and M. Gruebele. 2002a. Absolute comparison of simulated and experimental protein-folding dynamics. Nature. 420:102-106.
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
21
-
-
0037065310
-
The Tip cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
-
Snow, C. D., B. Zagrovic, and V. S. Pande. 2002b. The Tip cage: folding kinetics and unfolded state topology via molecular dynamics simulations. J. Am. Chem. Soc. 124:14548-14549.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 14548-14549
-
-
Snow, C.D.1
Zagrovic, B.2
Pande, V.S.3
-
22
-
-
0141990950
-
Effect of gatekeepers on the early folding kinetics of a model beta-barrel protein
-
Stoycheva, A. D., J. N. Onuchic, and C. L. Brooks, III. 2003. Effect of gatekeepers on the early folding kinetics of a model beta-barrel protein. J. Chem. Phys. 119:5722-5729.
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 5722-5729
-
-
Stoycheva, A.D.1
Onuchic, J.N.2
Brooks III, C.L.3
-
23
-
-
0035910479
-
The key to solving the protein-folding problem lies in an accurate description of the denatured state
-
van Gunsteren, W. F., R. Burgi, C. Peter, and X. Daura. 2001. The key to solving the protein-folding problem lies in an accurate description of the denatured state. Angew. Chem. Int. Ed. Engl. 40:352-355.
-
(2001)
Angew. Chem. Int. Ed. Engl.
, vol.40
, pp. 352-355
-
-
Van Gunsteren, W.F.1
Burgi, R.2
Peter, C.3
Daura, X.4
-
24
-
-
0242407127
-
Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like features
-
Zagrovic, B., and V. S. Pande. 2003. Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like features. Nat. Struct. Biol. 10:955-961.
-
(2003)
Nat. Struct. Biol.
, vol.10
, pp. 955-961
-
-
Zagrovic, B.1
Pande, V.S.2
-
25
-
-
0036394906
-
Native-like mean structure in the unfolded ensemble of small proteins
-
Zagrovic, B., C. Snow, S. Khaliq, M. Shirts, and V. Pande. 2002a. Native-like mean structure in the unfolded ensemble of small proteins. J. Mol. Biol. 323:153-164.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 153-164
-
-
Zagrovic, B.1
Snow, C.2
Khaliq, S.3
Shirts, M.4
Pande, V.5
-
26
-
-
0036428782
-
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
-
Zagrovic, B., C. D. Snow, M. R. Shirts, and V. S. Pande. 2002b. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323:927-937.
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 927-937
-
-
Zagrovic, B.1
Snow, C.D.2
Shirts, M.R.3
Pande, V.S.4
-
27
-
-
0035850758
-
Beta-hairpin folding simulations in atomistic detail using an implicit solvent model
-
Zagrovic, B., E. J. Sorin, and V. Pande. 2001. Beta-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.3
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