193 related articles for article (PubMed ID: 20849192)
1. Kinetics and mechanism of the unfolding native-to-loop transition of Trp-cage in explicit solvent via optimized forward flux sampling simulations.
Velez-Vega C; Borrero EE; Escobedo FA
J Chem Phys; 2010 Sep; 133(10):105103. PubMed ID: 20849192
[TBL] [Abstract][Full Text] [Related]
2. Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol.
Velez-Vega C; Borrero EE; Escobedo FA
J Chem Phys; 2009 Jun; 130(22):225101. PubMed ID: 19530790
[TBL] [Abstract][Full Text] [Related]
3. Reaction coordinates and transition pathways of rare events via forward flux sampling.
Borrero EE; Escobedo FA
J Chem Phys; 2007 Oct; 127(16):164101. PubMed ID: 17979313
[TBL] [Abstract][Full Text] [Related]
4. Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations.
Kannan S; Zacharias M
Proteins; 2009 Aug; 76(2):448-60. PubMed ID: 19173315
[TBL] [Abstract][Full Text] [Related]
5. Folding kinetics of a lattice protein via a forward flux sampling approach.
Borrero EE; Escobedo FA
J Chem Phys; 2006 Oct; 125(16):164904. PubMed ID: 17092136
[TBL] [Abstract][Full Text] [Related]
6. High-temperature unfolding of a trp-cage mini-protein: a molecular dynamics simulation study.
Seshasayee AS
Theor Biol Med Model; 2005 Mar; 2():7. PubMed ID: 15760474
[TBL] [Abstract][Full Text] [Related]
7. Optimizing the sampling and staging for simulations of rare events via forward flux sampling schemes.
Borrero EE; Escobedo FA
J Chem Phys; 2008 Jul; 129(2):024115. PubMed ID: 18624524
[TBL] [Abstract][Full Text] [Related]
8. Optimizing transition interface sampling simulations.
Borrero EE; Weinwurm M; Dellago C
J Chem Phys; 2011 Jun; 134(24):244118. PubMed ID: 21721623
[TBL] [Abstract][Full Text] [Related]
9. Unfolding transition state and intermediates of the tumor suppressor p16INK4a investigated by molecular dynamics simulations.
Interlandi G; Settanni G; Caflisch A
Proteins; 2006 Jul; 64(1):178-92. PubMed ID: 16596641
[TBL] [Abstract][Full Text] [Related]
10. The folding pathway of ubiquitin from all-atom molecular dynamics simulations.
Marianayagam NJ; Jackson SE
Biophys Chem; 2004 Oct; 111(2):159-71. PubMed ID: 15381313
[TBL] [Abstract][Full Text] [Related]
11. Rate constant and reaction coordinate of Trp-cage folding in explicit water.
Juraszek J; Bolhuis PG
Biophys J; 2008 Nov; 95(9):4246-57. PubMed ID: 18676648
[TBL] [Abstract][Full Text] [Related]
12. Hierarchy of folding and unfolding events of protein G, CI2, and ACBP from explicit-solvent simulations.
Camilloni C; Broglia RA; Tiana G
J Chem Phys; 2011 Jan; 134(4):045105. PubMed ID: 21280806
[TBL] [Abstract][Full Text] [Related]
13. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.
Paschek D; Nymeyer H; García AE
J Struct Biol; 2007 Mar; 157(3):524-33. PubMed ID: 17293125
[TBL] [Abstract][Full Text] [Related]
14. Folding of horse cytochrome c in the reduced state.
Bhuyan AK; Udgaonkar JB
J Mol Biol; 2001 Oct; 312(5):1135-60. PubMed ID: 11580255
[TBL] [Abstract][Full Text] [Related]
15. Transition network based on equilibrium sampling: a new method for extracting kinetic information from Monte Carlo simulations of protein folding.
Klenin KV; Wenzel W
J Chem Phys; 2011 Dec; 135(23):235105. PubMed ID: 22191905
[TBL] [Abstract][Full Text] [Related]
16. Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations.
Thukral L; Smith JC; Daidone I
J Am Chem Soc; 2009 Dec; 131(50):18147-52. PubMed ID: 19919102
[TBL] [Abstract][Full Text] [Related]
17. Thermodynamics and folding pathways of trpzip2: an accelerated molecular dynamics simulation study.
Yang L; Shao Q; Gao YQ
J Phys Chem B; 2009 Jan; 113(3):803-8. PubMed ID: 19113829
[TBL] [Abstract][Full Text] [Related]
18. Simulating the kinetics and thermodynamics of transitions via forward flux/umbrella sampling.
Borrero EE; Escobedo FA
J Phys Chem B; 2009 May; 113(18):6434-45. PubMed ID: 19402728
[TBL] [Abstract][Full Text] [Related]
19. Statistical mechanics of protein folding, unfolding and fluctuation.
Gło N
Adv Biophys; 1976; ():65-113. PubMed ID: 1015397
[TBL] [Abstract][Full Text] [Related]
20. Helix nucleation kinetics from molecular simulations in explicit solvent.
Hummer G; García AE; Garde S
Proteins; 2001 Jan; 42(1):77-84. PubMed ID: 11093262
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
