141 related articles for article (PubMed ID: 2025686)
1. Virtual rigid body dynamics.
Head-Gordon T; Brooks CL
Biopolymers; 1991 Jan; 31(1):77-100. PubMed ID: 2025686
[TBL] [Abstract][Full Text] [Related]
2. Molecular dynamics simulations of peptides and proteins with a continuum electrostatic model based on screened Coulomb potentials.
Hassan SA; Mehler EL; Zhang D; Weinstein H
Proteins; 2003 Apr; 51(1):109-25. PubMed ID: 12596268
[TBL] [Abstract][Full Text] [Related]
3. Separation of time scale and coupling in the motion governed by the coarse-grained and fine degrees of freedom in a polypeptide backbone.
Murarka RK; Liwo A; Scheraga HA
J Chem Phys; 2007 Oct; 127(15):155103. PubMed ID: 17949219
[TBL] [Abstract][Full Text] [Related]
4. Conformational dynamics of cytochrome c: correlation to hydrogen exchange.
García AE; Hummer G
Proteins; 1999 Aug; 36(2):175-91. PubMed ID: 10398365
[TBL] [Abstract][Full Text] [Related]
5. X-ray diffuse scattering and rigid-body motion in crystalline lysozyme probed by molecular dynamics simulation.
Héry S; Genest D; Smith JC
J Mol Biol; 1998 May; 279(1):303-19. PubMed ID: 9636718
[TBL] [Abstract][Full Text] [Related]
6. Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics.
Mathiowetz AM; Jain A; Karasawa N; Goddard WA
Proteins; 1994 Nov; 20(3):227-47. PubMed ID: 7892172
[TBL] [Abstract][Full Text] [Related]
7. An approximate method in using molecular mechanics simulations to study slow protein conformational changes.
Yang L; Gao YQ
J Phys Chem B; 2007 Mar; 111(11):2969-75. PubMed ID: 17319713
[TBL] [Abstract][Full Text] [Related]
8. Collective Langevin dynamics of conformational motions in proteins.
Lange OF; Grubmüller H
J Chem Phys; 2006 Jun; 124(21):214903. PubMed ID: 16774438
[TBL] [Abstract][Full Text] [Related]
9. Molecular dynamics of amicyanin reveals a conserved dynamical core for blue copper proteins.
Rizzuti B; Sportelli L; Guzzi R
Proteins; 2009 Mar; 74(4):961-71. PubMed ID: 18767164
[TBL] [Abstract][Full Text] [Related]
10. Elastic bag model for molecular dynamics simulations of solvated systems: application to liquid water and solvated peptides.
Li Y; Krilov G; Berne BJ
J Phys Chem B; 2006 Jul; 110(26):13256-63. PubMed ID: 16805640
[TBL] [Abstract][Full Text] [Related]
11. Dynamics of a protein and water molecules surrounding the protein: hydrogen-bonding between vibrating water molecules and a fluctuating protein.
Yoshioki S
J Comput Chem; 2002 Feb; 23(3):402-13. PubMed ID: 11908503
[TBL] [Abstract][Full Text] [Related]
12. [A turning point in the knowledge of the structure-function-activity relations of elastin].
Alix AJ
J Soc Biol; 2001; 195(2):181-93. PubMed ID: 11727705
[TBL] [Abstract][Full Text] [Related]
13. Estimating kinetic rates from accelerated molecular dynamics simulations: alanine dipeptide in explicit solvent as a case study.
de Oliveira CA; Hamelberg D; McCammon JA
J Chem Phys; 2007 Nov; 127(17):175105. PubMed ID: 17994855
[TBL] [Abstract][Full Text] [Related]
14. Partial rigid-body dynamics in NPT, NPAT and NPgammaT ensembles for proteins and membranes.
Ikeguchi M
J Comput Chem; 2004 Mar; 25(4):529-41. PubMed ID: 14735571
[TBL] [Abstract][Full Text] [Related]
15. Nonequilibrium, multiple-timescale simulations of ligand-receptor interactions in structured protein systems.
Zhang Y; Peters MH; Li Y
Proteins; 2003 Aug; 52(3):339-48. PubMed ID: 12866048
[TBL] [Abstract][Full Text] [Related]
16. Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach.
Gohlke H; Kuhn LA; Case DA
Proteins; 2004 Aug; 56(2):322-37. PubMed ID: 15211515
[TBL] [Abstract][Full Text] [Related]
17. A coarse-grained model for the formation of alpha helix with a noninteger period on simple cubic lattices.
Chen Y; Zhang Q; Ding J
J Chem Phys; 2006 May; 124(18):184903. PubMed ID: 16709135
[TBL] [Abstract][Full Text] [Related]
18. Ultrafast dynamics of hydrogen bond exchange in aqueous ionic solutions.
Park S; Odelius M; Gaffney KJ
J Phys Chem B; 2009 Jun; 113(22):7825-35. PubMed ID: 19435307
[TBL] [Abstract][Full Text] [Related]
19. Brownian dynamics simulation of helix-capping motifs.
Shen T; Wong CF; McCammon JA
Biopolymers; 2003 Oct; 70(2):252-9. PubMed ID: 14517913
[TBL] [Abstract][Full Text] [Related]
20. Assessing equilibration and convergence in biomolecular simulations.
Smith LJ; Daura X; van Gunsteren WF
Proteins; 2002 Aug; 48(3):487-96. PubMed ID: 12112673
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
