-
2
-
-
0043238073
-
Effects of confinement in chaperonin assisted protein folding: Rate enhancement by decreasing the roughness of the folding energy landscape
-
Baumketner A, Jewett A, Shea JE. 2003. Effects of confinement in chaperonin assisted protein folding: rate enhancement by decreasing the roughness of the folding energy landscape. J. Mol. Biol. 332:701-13
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 701-713
-
-
Baumketner, A.1
Jewett, A.2
Shea, J.E.3
-
3
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
ed. B Pullman. Dordrecht: Reidel
-
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. 1981. Interaction models for water in relation to protein hydration. In Intermolecular Forces, ed. B Pullman, pp. 331-42. Dordrecht: Reidel
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
4
-
-
0029151245
-
First-principles calculation of the folding free energy of a three-helix bundle protein
-
Boczko EM, Brooks CL III. 1995. First-principles calculation of the folding free energy of a three-helix bundle protein. Science 269:393-96
-
(1995)
Science
, vol.269
, pp. 393-396
-
-
Boczko, E.M.1
Brooks III, C.L.2
-
5
-
-
0142027789
-
Transition-path sampling of β-hairpin folding
-
Bolhuis PG. 2003. Transition-path sampling of β-hairpin folding. Proc. Natl. Acad. Sci. USA 100:12129-34
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12129-12134
-
-
Bolhuis, P.G.1
-
6
-
-
0036424048
-
Transition path sampling: Throwing ropes over rough mountain passes, in the dark
-
Bolhuis PG, Chandler D, Dellago C, Geissler PL. 2002. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu. Rev. Phys. Chem. 53:291-318
-
(2002)
Annu. Rev. Phys. Chem.
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
7
-
-
0036308818
-
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics
-
Borreguero JM, Dokholyan NV, Buldyrev SV, Shakhnovich EI, Stanley HE. 2002. Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J. Mol. Biol. 318: 863-76
-
(2002)
J. Mol. Biol.
, vol.318
, pp. 863-876
-
-
Borreguero, J.M.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Shakhnovich, E.I.4
Stanley, H.E.5
-
8
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimisation, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: a program for macromolecular energy, minimisation, and dynamics calculations. J. Comp. Chem. 4: 187-217
-
(1983)
J. Comp. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
9
-
-
0031005061
-
The energy landscape of a fast-folding protein mapped by Ala-Gly substitutions
-
Burton RE, Huang GS, Daugherty MA, Calderone TL, Oas TG. 1997. The energy landscape of a fast-folding protein mapped by Ala-Gly substitutions. Nat. Struct. Mol. Biol. 4:305-10
-
(1997)
Nat. Struct. Mol. Biol.
, vol.4
, pp. 305-310
-
-
Burton, R.E.1
Huang, G.S.2
Daugherty, M.A.3
Calderone, T.L.4
Oas, T.G.5
-
10
-
-
0037093655
-
Weak temperature dependence of the free energy surface and folding pathways of structured peptides
-
Cavalli A, Ferrara P, Caflisch A. 2002. Weak temperature dependence of the free energy surface and folding pathways of structured peptides. Proteins 47:305-14
-
(2002)
Proteins
, vol.47
, pp. 305-314
-
-
Cavalli, A.1
Ferrara, P.2
Caflisch, A.3
-
11
-
-
3142782241
-
Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates
-
Chavez LL, Onuchic JN, Clementi C. 2004. Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates. J Am. Chem. Soc. 126:8426-32
-
(2004)
J Am. Chem. Soc.
, vol.126
, pp. 8426-8432
-
-
Chavez, L.L.1
Onuchic, J.N.2
Clementi, C.3
-
12
-
-
0034705115
-
How native-state topology affects the folding of dihydrofolate reductase and interleukin-1 beta
-
Clementi C, Jennings PA, Onuchic JN. 2000. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1 beta. Proc. Natl. Acad. Sci. USA 97:5871-76
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 5871-5876
-
-
Clementi, C.1
Jennings, P.A.2
Onuchic, J.N.3
-
13
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and "enroute" intermediates for protein folding? An investigation for small globular proteins
-
Clementi C, Nymeyer H, Onuchic JN. 2000. Topological and energetic factors: What determines the structural details of the transition state ensemble and "enroute" intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 298:937-53
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
14
-
-
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, et al. 1995. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117:5179-97
-
(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
-
15
-
-
0026525048
-
Molecular dynamics simulations of helix denaturation
-
Daggett V, Levitt M. 1992. Molecular dynamics simulations of helix denaturation. J. Mol Biol. 223:1121-38
-
(1992)
J. Mol Biol.
, vol.223
, pp. 1121-1138
-
-
Daggett, V.1
Levitt, M.2
-
16
-
-
0027219504
-
Protein unfolding pathways explored through molecular dynamics simulations
-
Daggett V, Levitt M. 1993. Protein unfolding pathways explored through molecular dynamics simulations. J. Mol. Biol. 232:600-19
-
(1993)
J. Mol. Biol.
, vol.232
, pp. 600-619
-
-
Daggett, V.1
Levitt, M.2
-
17
-
-
0032539209
-
Combined molecular dynamics and Phi-value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: Structural basis of Hammond and anti-Hammond effects
-
Daggett V, Li A, Fersht AR. 1998. Combined molecular dynamics and Phi-value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: structural basis of Hammond and anti-Hammond effects. J. Am. Chem. Soc. 120:12740-54
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 12740-12754
-
-
Daggett, V.1
Li, A.2
Fersht, A.R.3
-
18
-
-
0036968512
-
Increasing temperature accelerates protein unfolding without changing the pathway of unfolding
-
Day R, Bennion BJ, Ham S, Daggett V. 2002. Increasing temperature accelerates protein unfolding without changing the pathway of unfolding. J. Mol. Biol. 322: 189-203
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 189-203
-
-
Day, R.1
Bennion, B.J.2
Ham, S.3
Daggett, V.4
-
19
-
-
0032917075
-
De novo design of a monomeric three-stranded antiparallel beta-sheet
-
De Alba E, Santoro J, Rico M, Jimenez MA. 1999. De novo design of a monomeric three-stranded antiparallel beta-sheet. Protein Sci. 8:854-65
-
(1999)
Protein Sci.
, vol.8
, pp. 854-865
-
-
De Alba, E.1
Santoro, J.2
Rico, M.3
Jimenez, M.A.4
-
20
-
-
0036306054
-
Probing the energy landscape of protein folding/unfolding transition states
-
De Jong D, Riley R, Alonso DO, Daggett V. 2002. Probing the energy landscape of protein folding/unfolding transition states. J. Mol. Biol. 319:229-42
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 229-242
-
-
De Jong, D.1
Riley, R.2
Alonso, D.O.3
Daggett, V.4
-
22
-
-
0001691450
-
Protein fold determination from sparse distance restraints: The restrained generic protein direct Monte Carlo method
-
Debe DA, Carlson MJ, Sadanobu J, Chan SI, Goddard WA. 1999. Protein fold determination from sparse distance restraints: the restrained generic protein direct Monte Carlo method. J. Phys. Chem. B 103:3001-8
-
(1999)
J. Phys. Chem. B
, vol.103
, pp. 3001-3008
-
-
Debe, D.A.1
Carlson, M.J.2
Sadanobu, J.3
Chan, S.I.4
Goddard, W.A.5
-
23
-
-
0033521194
-
First principles prediction of protein folding rates
-
Debe DA, Goddard WA. 1999. First principles prediction of protein folding rates. J. Mol. Biol. 294:619-25
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 619-625
-
-
Debe, D.A.1
Goddard, W.A.2
-
24
-
-
0033578828
-
Is protein unfolding the reverse of protein folding? A lattice simulation analysis
-
Dinner AR, Karplus M. 1999. Is protein unfolding the reverse of protein folding? A lattice simulation analysis. J. Mol. Biol. 292:403-19
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 403-419
-
-
Dinner, A.R.1
Karplus, M.2
-
25
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du R, Pande VS, Grosberg AY, Tanaka R, Shakhnovich EI. 1997. On the transition coordinate for protein folding. J. Chem. Phys. 108:334-50
-
(1997)
J. Chem. Phys.
, vol.108
, pp. 334-350
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, R.4
Shakhnovich, E.I.5
-
26
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman PA. 1998. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282:740-44
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
27
-
-
17444404720
-
Foldamer simulations: Novel computational methods and applications to poly-phenylacetylene oligomers
-
Elmer SP, Pande VS. 2004. Foldamer simulations: novel computational methods and applications to poly-phenylacetylene oligomers. J. Chem. Phys. 121:12760-71
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 12760-12771
-
-
Elmer, S.P.1
Pande, V.S.2
-
28
-
-
0001767031
-
Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations
-
Ferrara P, Apostolakis J, Caflisch A. 2000. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B 104:5000-10
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 5000-5010
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
29
-
-
0036138028
-
Evaluation of a fast implicit solvent model for molecular dynamics simulations
-
Ferrara P, Apostolakis J, Caflisch A. 2002. Evaluation of a fast implicit solvent model for molecular dynamics simulations. Proteins 46:24-33
-
(2002)
Proteins
, vol.46
, pp. 24-33
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
30
-
-
0034718553
-
Folding simulations of a three-stranded antiparallel β-sheet peptide
-
Ferrara P, Caflisch A. 2000. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl. Acad. Sci. USA 97:10780-85
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
31
-
-
0035793713
-
Native topology or specific interactions: What is more important for protein folding?
-
Ferrara P, Caflisch A. 2001. Native topology or specific interactions: What is more important for protein folding? J. Mol. Biol. 306:837-50
-
(2001)
J. Mol. Biol.
, vol.306
, pp. 837-850
-
-
Ferrara, P.1
Caflisch, A.2
-
33
-
-
0037195097
-
On the simulation of protein folding by short time scale molecular dynamics and distributed computing
-
Fersht AR. 2002. On the simulation of protein folding by short time scale molecular dynamics and distributed computing. Proc. Natl. Acad. Sci. USA 99:14122-25
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 14122-14125
-
-
Fersht, A.R.1
-
34
-
-
0023662562
-
Structure-activity relationships in engineered proteins: Analysis of use of binding energy by linear free energy relationships
-
Fersht AR, Leatherbarrow RJ, Wells TNC. 1987. Structure-activity relationships in engineered proteins: analysis of use of binding energy by linear free energy relationships. Biochemistry 26:6030-38
-
(1987)
Biochemistry
, vol.26
, pp. 6030-6038
-
-
Fersht, A.R.1
Leatherbarrow, R.J.2
Wells, T.N.C.3
-
35
-
-
2542599277
-
Phi-value analysis and the nature of protein-folding transition states
-
Fersht AR, Sato S. 2004. Phi-value analysis and the nature of protein-folding transition states. Proc. Natl. Acad. Sci. USA 101:7976-81
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 7976-7981
-
-
Fersht, A.R.1
Sato, S.2
-
36
-
-
0030775114
-
Can protein unfolding simulate protein folding?
-
Finkelstein AV. 1997. Can protein unfolding simulate protein folding? Protein Eng. 10:843-45
-
(1997)
Protein Eng.
, vol.10
, pp. 843-845
-
-
Finkelstein, A.V.1
-
37
-
-
0037157317
-
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
-
Fukunishi H, Watanabe O, Takada S. 2002. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction. J. Chem. Phys. 116:9058-67
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 9058-9067
-
-
Fukunishi, H.1
Watanabe, O.2
Takada, S.3
-
38
-
-
0032812796
-
Mapping the interactions present in the transition state for unfolding/folding of FKBP12
-
Fulton KF, Main ERG, Daggett V, Jackson SE. 1999. Mapping the interactions present in the transition state for unfolding/folding of FKBP12. J. Mol. Biol. 291:445-61
-
(1999)
J. Mol. Biol.
, vol.291
, pp. 445-461
-
-
Fulton, K.F.1
Main, E.R.G.2
Daggett, V.3
Jackson, S.E.4
-
39
-
-
0345133287
-
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
-
García AE, Onuchic JN. 2003. Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc. Natl Acad. Sci. USA 100:13898-903
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 13898-13903
-
-
García, A.E.1
Onuchic, J.N.2
-
40
-
-
0345255608
-
Unifying features in protein-folding mechanisms
-
Gianni S, Guydosh NR, Khan F, Caldas TD, Mayor U, et al. 2003. Unifying features in protein-folding mechanisms. Proc. Nad. Acad. Sci. USA 100:13286-91
-
(2003)
Proc. Nad. Acad. Sci. USA
, vol.100
, pp. 13286-13291
-
-
Gianni, S.1
Guydosh, N.R.2
Khan, F.3
Caldas, T.D.4
Mayor, U.5
-
41
-
-
0037076334
-
Molecular dynamics simulations of protein folding from the transition state
-
Gsponer J, Caflisch A. 2002. Molecular dynamics simulations of protein folding from the transition state. Proc. Natl. Acad. Sci. USA 99:6719-24
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 6719-6724
-
-
Gsponer, J.1
Caflisch, A.2
-
43
-
-
8644232696
-
Combinatorial modeling of protein folding kinetics: Free energy profiles and rates
-
Henry ER, Eaton WA. 2004. Combinatorial modeling of protein folding kinetics: free energy profiles and rates. Chem. Phys. 307:163-85
-
(2004)
Chem. Phys.
, vol.307
, pp. 163-185
-
-
Henry, E.R.1
Eaton, W.A.2
-
45
-
-
2942622288
-
Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew
-
Horn HW, Swope WC, Pitera JW, Madura JD, Dick TJ, et al. 2004. Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew. J. Chem. Phys. 120:9665-78
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 9665-9678
-
-
Horn, H.W.1
Swope, W.C.2
Pitera, J.W.3
Madura, J.D.4
Dick, T.J.5
-
46
-
-
2942590388
-
Simulation, experiment, and evolution: Understanding nucleation in protein S6 folding
-
Hubner IA, Oliveberg M, Shakhnovich EI. 2004. Simulation, experiment, and evolution: understanding nucleation in protein S6 folding. Proc. Natl. Acad. Sci. USA 101:8354-59
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 8354-8359
-
-
Hubner, I.A.1
Oliveberg, M.2
Shakhnovich, E.I.3
-
47
-
-
0842332830
-
Commitment and nucleation in the protein G transition state
-
Hubner IA, Shimada J, Shakhnovich EI. 2004. Commitment and nucleation in the protein G transition state. J. Mol. Biol. 336:745-61
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 745-761
-
-
Hubner, I.A.1
Shimada, J.2
Shakhnovich, E.I.3
-
48
-
-
0034683242
-
Conformational diffusion and helix formation kinetics
-
Hummer G, García AE, Garde S. 2000. Conformational diffusion and helix formation kinetics. Phys. Rev. Lett. 85:2637-40
-
(2000)
Phys. Rev. Lett.
, vol.85
, pp. 2637-2640
-
-
Hummer, G.1
García, A.E.2
Garde, S.3
-
49
-
-
0035179018
-
Helix nucleation kinetics from molecular simulations in explicit solvent
-
Hummer G, García AE, Garde S. 2001. Helix nucleation kinetics from molecular simulations in explicit solvent. Proteins 42:77-84
-
(2001)
Proteins
, vol.42
, pp. 77-84
-
-
Hummer, G.1
García, A.E.2
Garde, S.3
-
50
-
-
2942689229
-
Prediction of protein folding rates from the amino acid sequence-predicted secondary structure
-
Ivankov DN, Finkelstein AV. 2004. Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Proc. Natl. Acad. Sci. USA 101:8942-44
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 8942-8944
-
-
Ivankov, D.N.1
Finkelstein, A.V.2
-
51
-
-
0037042264
-
Molecular dynamics study of peptides in implicit water: Ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif
-
Jang S, Shin S, Pak Y. 2002. Molecular dynamics study of peptides in implicit water: ab initio folding of beta-hairpin, beta-sheet, and beta beta alpha-motif. J. Am. Chem. Soc. 124:4976-77
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 4976-4977
-
-
Jang, S.1
Shin, S.2
Pak, Y.3
-
52
-
-
0141976331
-
Replica-exchange method using the generalized effective potential
-
Jang S, Shin S, Pak Y. 2003. Replica-exchange method using the generalized effective potential. Phys. Rev. Lett. 91: 058305
-
(2003)
Phys. Rev. Lett.
, vol.91
, pp. 058305
-
-
Jang, S.1
Shin, S.2
Pak, Y.3
-
53
-
-
20544461014
-
-
Deleted in proof
-
Deleted in proof
-
-
-
-
54
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-35
-
(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
-
55
-
-
0029912748
-
Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, Tirado-Rives J. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118:11225-36
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
56
-
-
33645941402
-
The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin
-
Jorgensen WL, Tirado-Rives J. 1988. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-66
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
57
-
-
20544469320
-
-
Deleted in proof
-
Deleted in proof
-
-
-
-
58
-
-
0037062480
-
Simulations of β-hairpin folding confined to spherical pores using distributed computing
-
Klimov DK, Newfield D, Thirumalai D. 2002. Simulations of β-hairpin folding confined to spherical pores using distributed computing. Proc. Natl. Acad. Sci. USA 99:8019-24
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 8019-8024
-
-
Klimov, D.K.1
Newfield, D.2
Thirumalai, D.3
-
59
-
-
0035850732
-
Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model
-
Koga N, Takada S. 2001. Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model. J. Mol. Biol. 313:171-80
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
60
-
-
1442348207
-
Discerning the structure and energy of multiple transition states in protein folding using Psi-analysis
-
Krantz BA, Dothager RS, Sosnick TR. 2004. Discerning the structure and energy of multiple transition states in protein folding using Psi-analysis. J. Mol. Biol. 337:463-75
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 463-475
-
-
Krantz, B.A.1
Dothager, R.S.2
Sosnick, T.R.3
-
61
-
-
0043237588
-
Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding
-
Krieger F, Fierz B, Bien O, Drewello M, Kiefhaber T. 2003. Dynamics of unfolded polypeptide chains as model for the earliest steps in protein folding. J. Mol. Biol. 332:265-74
-
(2003)
J. Mol. Biol.
, vol.332
, pp. 265-274
-
-
Krieger, F.1
Fierz, B.2
Bien, O.3
Drewello, M.4
Kiefhaber, T.5
-
62
-
-
0038054301
-
Experimental tests of villin subdomain folding simulations
-
a. Kubelka J, Eaton WA, Hofrichter J. 2003. Experimental tests of villin subdomain folding simulations. J. Mol. Biol. 329:625-30
-
(2003)
J. Mol. Biol.
, vol.329
, pp. 625-630
-
-
Kubelka, J.1
Eaton, W.A.2
Hofrichter, J.3
-
63
-
-
0032555115
-
Synergy between simulation and experiment in describing the energy landscape of protein folding
-
Ladurner AG, Itzhaki LS, Daggett V, Fersht AR. 1998. Synergy between simulation and experiment in describing the energy landscape of protein folding. Proc. Natl. Acad. Sci. USA 95:8473-78
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 8473-8478
-
-
Ladurner, A.G.1
Itzhaki, L.S.2
Daggett, V.3
Fersht, A.R.4
-
64
-
-
0034691198
-
Measuring the rate of intramolecular contact formation in polypeptides
-
Lapidus LJ, EatonWA, Hofrichter J. 2000. Measuring the rate of intramolecular contact formation in polypeptides. Proc. Natl. Acad. Sci. USA 97:7220-25
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 7220-7225
-
-
Lapidus, L.J.1
Eaton, W.A.2
Hofrichter, J.3
-
65
-
-
1442300067
-
Roles of physical interactions in determining protein-folding mechanisms: Molecular simulation of protein G and alpha spectrin SH3
-
Lee SY, Fujitsuka Y, Kim do H, Takada S. 2004. Roles of physical interactions in determining protein-folding mechanisms: molecular simulation of protein G and alpha spectrin SH3. Proteins 55:128-38
-
(2004)
Proteins
, vol.55
, pp. 128-138
-
-
Lee, S.Y.1
Fujitsuka, Y.2
Kim Do, H.3
Takada, S.4
-
67
-
-
0000125216
-
Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt M, Hirshberg M, Sharon R, Laidig KE, Daggett V. 1997. Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution. J. Phys. Chem. B 101:5051-61
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5051-5061
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Laidig, K.E.4
Daggett, V.5
-
68
-
-
0028143603
-
Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
-
Li A, Daggett V. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics: chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci USA 91:10430-34
-
(1994)
Proc. Natl. Acad. Sci USA
, vol.91
, pp. 10430-10434
-
-
Li, A.1
Daggett, V.2
-
69
-
-
0029963345
-
Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
-
Li A, Daggett V. 1996. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 257:412-29
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 412-429
-
-
Li, A.1
Daggett, V.2
-
70
-
-
0032579189
-
Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate
-
Li A, Daggett V. 1998. Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J. Mol. Biol. 275:677-94
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 677-694
-
-
Li, A.1
Daggett, V.2
-
71
-
-
0035818481
-
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations
-
Li L, Shakhnovich EI. 2001. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc. Natl. Acad. Sci. USA 98:13014-18
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 13014-13018
-
-
Li, L.1
Shakhnovich, E.I.2
-
72
-
-
1642444204
-
Ubiquitin-like protein domains show high resistance to mechanical unfolding similar to that of the 127 domain in titin: Evidence from simulations
-
Li PC, Makarov DE. 2004. Ubiquitin-like protein domains show high resistance to mechanical unfolding similar to that of the 127 domain in titin: evidence from simulations. J. Phys. Chem. B 108:745-49
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 745-749
-
-
Li, P.C.1
Makarov, D.E.2
-
73
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 102:3586-616
-
(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
-
74
-
-
0037133574
-
How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
-
Makarov DE, Keller CA, Plaxco KW, Metiu H. 2002. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc. Natl. Acad. Sci. USA 99:3535-39
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 3535-3539
-
-
Makarov, D.E.1
Keller, C.A.2
Plaxco, K.W.3
Metiu, H.4
-
75
-
-
0037155403
-
A model for the kinetics of protein folding: Kinetic Monte Carlo simulations and analytical results
-
Makarov DE, Metiu H. 2002. A model for the kinetics of protein folding: kinetic Monte Carlo simulations and analytical results. J. Chem. Phys. 116:5205-16
-
(2002)
J. Chem. Phys.
, vol.116
, pp. 5205-5216
-
-
Makarov, D.E.1
Metiu, H.2
-
76
-
-
0037456298
-
The complete folding pathway of a protein from nanoseconds to microseconds
-
Mayor U, Guydosh NR, Johnson CM, Grossmann JG, Sato S, et al. 2003. The complete folding pathway of a protein from nanoseconds to microseconds. Nature 421:863-67
-
(2003)
Nature
, vol.421
, pp. 863-867
-
-
Mayor, U.1
Guydosh, N.R.2
Johnson, C.M.3
Grossmann, J.G.4
Sato, S.5
-
77
-
-
0034610360
-
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
-
Mayor U, Johnson CM, Daggett V, Fersht AR. 2000. Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation. Proc. Natl. Acad. Sci. USA 97:13518-22
-
(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
-
78
-
-
0034864528
-
Generalized-ensemble algorithms formolecular simulations of biopolymers
-
Mitsutake A, Sugita Y, Okamoto Y. 2001. Generalized-ensemble algorithms formolecular simulations of biopolymers. Biopolymers 60:96-123
-
(2001)
Biopolymers
, vol.60
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
79
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
Muñoz V, Eaton WA. 1999. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl. Acad. Sci. USA 96:11311-16
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11311-11316
-
-
Muñoz, V.1
Eaton, W.A.2
-
81
-
-
0037478676
-
Analysis of the distributed computing approach applied to the folding of a small beta peptide
-
Paci E, Cavalli A, Vendruscolo M, Caflisch A. 2003. Analysis of the distributed computing approach applied to the folding of a small beta peptide. Proc. Natl. Acad. Sci. USA 100:8217-22
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 8217-8222
-
-
Paci, E.1
Cavalli, A.2
Vendruscolo, M.3
Caflisch, A.4
-
82
-
-
0035814880
-
Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: Free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding
-
Pan Y, Daggett V. 2001. Direct comparison of experimental and calculated folding free energies for hydrophobic deletion mutants of chymotrypsin inhibitor 2: free energy perturbation calculations using transition and denatured states from molecular dynamics simulations of unfolding. Biochemistry 40:2723-31
-
(2001)
Biochemistry
, vol.40
, pp. 2723-2731
-
-
Pan, Y.1
Daggett, V.2
-
83
-
-
0037235952
-
Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing
-
Pande VS, Baker I, Chapman J, Elmer S, Kaliq S, et al. 2003. Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing. Biopolymers 68:91-109
-
(2003)
Biopolymers
, vol.68
, pp. 91-109
-
-
Pande, V.S.1
Baker, I.2
Chapman, J.3
Elmer, S.4
Kaliq, S.5
-
84
-
-
0037934616
-
Understanding folding and design: Replica-exchange simulations of "Trp-cage" fly miniproteins
-
Pitera JW, Swope W. 2003. Understanding folding and design: replica-exchange simulations of "Trp-cage" fly miniproteins. Proc. Natl. Acad. Sci. USA 100:7587-92
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 7587-7592
-
-
Pitera, J.W.1
Swope, W.2
-
85
-
-
0032506017
-
Limited internal friction in the rate-limiting step of a two-state protein folding reaction
-
Plaxco KW, Baker D. 1998. Limited internal friction in the rate-limiting step of a two-state protein folding reaction. Proc. Natl Acad. Sci. USA 95:13591-96
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 13591-13596
-
-
Plaxco, K.W.1
Baker, D.2
-
86
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco KW, Simons KT, Baker D. 1998. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol 277:985-94
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
87
-
-
0034687123
-
Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
-
Plaxco KW, Simons KT, Ruczinski I, David B. 2000. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 39:11177-83
-
(2000)
Biochemistry
, vol.39
, pp. 11177-11183
-
-
Plaxco, K.W.1
Simons, K.T.2
Ruczinski, I.3
David, B.4
-
88
-
-
4043171970
-
The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii
-
Qiu D, Shenkin PS, Hollinger FP, Still WC. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Born radii. J. Phys. Chem. A 101:3005-14
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 3005-3014
-
-
Qiu, D.1
Shenkin, P.S.2
Hollinger, F.P.3
Still, W.C.4
-
89
-
-
0037305918
-
Multiplexed-replica exchange molecular dynamics method for protein folding simulation
-
Rhee YM, Pande VS. 2003. Multiplexed-replica exchange molecular dynamics method for protein folding simulation. Biophys. J. 84:775-86
-
(2003)
Biophys. J.
, vol.84
, pp. 775-786
-
-
Rhee, Y.M.1
Pande, V.S.2
-
90
-
-
2342448436
-
Simulations of the role of water in the protein-folding mechanism
-
Rhee YM, Sorin EJ, Jayachandran G, Lindahl E, Pande VS. 2004. Simulations of the role of water in the protein-folding mechanism. Proc. Natl. Acad. Sci. USA 101:6456-61
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6456-6461
-
-
Rhee, Y.M.1
Sorin, E.J.2
Jayachandran, G.3
Lindahl, E.4
Pande, V.S.5
-
91
-
-
0036467163
-
Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics
-
Sanbonmatsu KY, Garcia AE. 2002. Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins 46:225-34
-
(2002)
Proteins
, vol.46
, pp. 225-234
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
92
-
-
0345304461
-
Origin of unusual phi-values in protein folding: Evidence against specific nucleation sites
-
Sanchez IE, Kiefhaber T. 2003. Origin of unusual phi-values in protein folding: evidence against specific nucleation sites. J. Mol. Biol. 334:1077-85
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 1077-1085
-
-
Sanchez, I.E.1
Kiefhaber, T.2
-
94
-
-
0026579572
-
The folding of an enzyme. IH. Structure of the transition state for unfolding of barnase analyzed by a protein engineering procedure
-
Serrano L, Matouschek A, Fersht AR. 1992. The folding of an enzyme. IH. Structure of the transition state for unfolding of barnase analyzed by a protein engineering procedure. J. Mol. Biol. 224:805-18
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 805-818
-
-
Serrano, L.1
Matouschek, A.2
Fersht, A.R.3
-
95
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea JE, Brooks CL 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
-
96
-
-
0033607208
-
Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A
-
Shea JE, Onuchic JN, Brooks CL III. 1999. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc. Natl Acad. Sci. USA 96:12512-17
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 12512-12517
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks III, C.L.3
-
97
-
-
0037058992
-
Probing the folding free energy landscape of the Src-SH3 protein domain
-
Shea JE, Onuchic JN, Brooks CL III. 2002. Probing the folding free energy landscape of the Src-SH3 protein domain. Proc. Natl. Acad. Sci. USA 99:16064-68
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 16064-16068
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks III, C.L.3
-
98
-
-
0032080053
-
Calculations on folding of segment B1 of streptococcal protein G
-
Sheinerman FB, Brooks CL III. 1998. Calculations on folding of segment B1 of streptococcal protein G. J. Mol. Biol. 278:439-56
-
(1998)
J. Mol. Biol.
, vol.278
, pp. 439-456
-
-
Sheinerman, F.B.1
Brooks III, C.L.2
-
99
-
-
0032539561
-
Molecular picture of folding of a small alpha/beta protein
-
Sheinerman FB, Brooks CL III. 1998. Molecular picture of folding of a small alpha/beta protein. Proc. Natl. Acad. Sci. USA 95:1562-67
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 1562-1567
-
-
Sheinerman, F.B.1
Iii, B.C.L.2
-
100
-
-
0037143694
-
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation
-
Shimada J, Shakhnovich EI. 2002. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc. Natl. Acad. Sci. USA 99:11175-80
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11175-11180
-
-
Shimada, J.1
Shakhnovich, E.I.2
-
101
-
-
0035962955
-
Mathematical analysis of coupled parallel simulations
-
Shirts MR, Pande VS. 2001. Mathematical analysis of coupled parallel simulations. Phys. Rev. Lett. 86:4983-87
-
(2001)
Phys. Rev. Lett.
, vol.86
, pp. 4983-4987
-
-
Shirts, M.R.1
Pande, V.S.2
-
102
-
-
0037174385
-
All-atom structure prediction and folding simulations of a stable protein
-
Simmerling C, Strockbine B, Roitberg AE. 2002. All-atom structure prediction and folding simulations of a stable protein. J. Am. Chem. Soc. 124:11258-59
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 11258-11259
-
-
Simmerling, C.1
Strockbine, B.2
Roitberg, A.E.3
-
103
-
-
3142707288
-
Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin
-
Singhal N, Snow CD, Pande VS. 2004. Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin. J. Chem. Phys. 121:415-25
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 415-425
-
-
Singhal, N.1
Snow, C.D.2
Pande, V.S.3
-
104
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow CD, Nguyen H, Pande VS, Gruebele M. 2002. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420:102-6
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
105
-
-
1642570290
-
Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy
-
Snow CD, Qiu L, Du D, Gai F, Hagen SJ, Pande VS. 2004. Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. Proc. Natl. Acad. Sci. USA 101:4077-82
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4077-4082
-
-
Snow, C.D.1
Qiu, L.2
Du, D.3
Gai, F.4
Hagen, S.J.5
Pande, V.S.6
-
106
-
-
20544435097
-
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
-
In press
-
Sorin EJ, Pande VS. 2005. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophys. J. In press
-
(2005)
Biophys. J.
-
-
Sorin, E.J.1
Pande, V.S.2
-
107
-
-
0042845840
-
Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations
-
Sorin EJ, Rhee YM, Nakatani BJ, Pande VS. 2003. Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations. Biophys. J. 85:790-803
-
(2003)
Biophys. J.
, vol.85
, pp. 790-803
-
-
Sorin, E.J.1
Rhee, Y.M.2
Nakatani, B.J.3
Pande, V.S.4
-
108
-
-
0034294024
-
Multidimensional replica-exchange method for free-energy calculations
-
Sugita Y, Kitao A, Okamoto Y. 2000. Multidimensional replica-exchange method for free-energy calculations. J. Chem. Phys. 113:6042-51
-
(2000)
J. Chem. Phys.
, vol.113
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
109
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita Y, Okamoto Y. 1999. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 314: 141-51
-
(1999)
Chem. Phys. Lett.
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
110
-
-
2942567954
-
Describing protein folding kinetics by molecular dynamics simulations. 1. Theory
-
Swope WC, Pitera JW, Suits FJ. 2004. Describing protein folding kinetics by molecular dynamics simulations. 1. Theory. J. Phys. Chem. B 108:6571-81
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6571-6581
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.J.3
-
111
-
-
2942560604
-
Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and a beta-hairpin peptide
-
Swope WC, Pitera JW, Suits FJ, Pitman M, Eleftheriou M, et al. 2004. Describing protein folding kinetics by molecular dynamics simulations. 2. Example applications to alanine dipeptide and a beta-hairpin peptide. J. Phys. Chem. B 108:6582-94
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6582-6594
-
-
Swope, W.C.1
Pitera, J.W.2
Suits, F.J.3
Pitman, M.4
Eleftheriou, M.5
-
112
-
-
0000137407
-
The helix-coil kinetics of a heteropeptide
-
Thompson PA, Munoz V, Jas GS, Henry ER, Eaton WA, Hofrichter J. 2000. The helix-coil kinetics of a heteropeptide. J. Phys. Chem. B 104:378-89
-
(2000)
J. Phys. Chem. B
, vol.104
, pp. 378-389
-
-
Thompson, P.A.1
Munoz, V.2
Jas, G.S.3
Henry, E.R.4
Eaton, W.A.5
Hofrichter, J.6
-
113
-
-
0030046906
-
Fast events in protein folding: Helix melting and formation in a small peptide
-
Williams S, Causgrove TP, Gilmanshin R, Fang KS, Callender RH, et al. 1996. Fast events in protein folding: helix melting and formation in a small peptide. Biochemistry 35:691-97
-
(1996)
Biochemistry
, vol.35
, pp. 691-697
-
-
Williams, S.1
Causgrove, T.P.2
Gilmanshin, R.3
Fang, K.S.4
Callender, R.H.5
-
114
-
-
2342525803
-
Latest folding game results: Protein A barely frustrates computationalists
-
Wolynes PG. 2004. Latest folding game results: Protein A barely frustrates computationalists. Proc. Natl. Acad. Sci. USA 101:6837-38
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6837-6838
-
-
Wolynes, P.G.1
-
115
-
-
0037067120
-
Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent
-
Yeh I-C, Hummer G. 2002. Peptide loop-closure kinetics from microsecond molecular dynamics simulations in explicit solvent. J. Am. Chem. Soc. 124:6563-68
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 6563-6568
-
-
Yeh, I.-C.1
Hummer, G.2
-
116
-
-
84948512335
-
On the approximation of solvent effects on the conformation and dynamics of cyclosporin a by stochastic dynamics simulation techniques
-
Yun-yu S, Wang L, Gunsteren WFV. 1988. On the approximation of solvent effects on the conformation and dynamics of cyclosporin A by stochastic dynamics simulation techniques. Mol. Simul. 1:369-83
-
(1988)
Mol. Simul.
, vol.1
, pp. 369-383
-
-
Yun-yu, S.1
Wang, L.2
Gunsteren, W.F.V.3
-
117
-
-
0042561888
-
Solvent viscosity dependence of the folding rate of a small protein: Distributed computing study
-
Zagrovic B, Pande V. 2003. Solvent viscosity dependence of the folding rate of a small protein: distributed computing study. J. Comp. Chem. 24:1432-36
-
(2003)
J. Comp. Chem.
, vol.24
, pp. 1432-1436
-
-
Zagrovic, B.1
Pande, V.2
-
118
-
-
0036428782
-
Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing
-
Zagrovic B, Snow CD, Shirts MR, Pande VS. 2002. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 323:927-37
-
(2002)
J. Mol. Biol.
, vol.323
, pp. 927-937
-
-
Zagrovic, B.1
Snow, C.D.2
Shirts, M.R.3
Pande, V.S.4
-
119
-
-
0035850758
-
β-hairpin folding simulations in atomistic detail using an implicit solvent model
-
Zagrovic B, Sorin EJ, Pande V. 2001. β-hairpin folding simulations in atomistic detail using an implicit solvent model. J. Mol. Biol. 313:151-69
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 151-169
-
-
Zagrovic, B.1
Sorin, E.J.2
Pande, V.3
-
120
-
-
0141704162
-
Free energy landscape of protein folding in water: Explicit versus implicit solvent
-
Zhou RH. 2003. Free energy landscape of protein folding in water: explicit versus implicit solvent. Proteins 53:148-61
-
(2003)
Proteins
, vol.53
, pp. 148-161
-
-
Zhou, R.H.1
-
121
-
-
0036789950
-
Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water?
-
Zhou RH, Berne BJ. 2002. Can a continuum solvent model reproduce the free energy landscape of a beta-hairpin folding in water? Proc. Natl. Acad. Sci. USA 99:12777-82
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 12777-12782
-
-
Zhou, R.H.1
Berne, B.J.2
-
122
-
-
0035909921
-
The free energy landscape for beta hairpin folding in explicit water
-
Zhou RH, Berne BJ, Germain R. 2001. The free energy landscape for beta hairpin folding in explicit water. Proc. Natl. Acad. Sci. USA 98:14931-36
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 14931-14936
-
-
Zhou, R.H.1
Berne, B.J.2
Germain, R.3
|