148 related articles for article (PubMed ID: 21425286)
1. Theory for trivial trajectory parallelization of multicanonical molecular dynamics and application to a polypeptide in water.
Ikebe J; Umezawa K; Kamiya N; Sugihara T; Yonezawa Y; Takano Y; Nakamura H; Higo J
J Comput Chem; 2011 May; 32(7):1286-97. PubMed ID: 21425286
[TBL] [Abstract][Full Text] [Related]
2. A virtual-system coupled multicanonical molecular dynamics simulation: principles and applications to free-energy landscape of protein-protein interaction with an all-atom model in explicit solvent.
Higo J; Umezawa K; Nakamura H
J Chem Phys; 2013 May; 138(18):184106. PubMed ID: 23676028
[TBL] [Abstract][Full Text] [Related]
3. Simple and effective application of the Wang-Landau method for multicanonical molecular dynamics simulation.
Shimoyama H; Nakamura H; Yonezawa Y
J Chem Phys; 2011 Jan; 134(2):024109. PubMed ID: 21241082
[TBL] [Abstract][Full Text] [Related]
4. Adaptive lambda square dynamics simulation: an efficient conformational sampling method for biomolecules.
Ikebe J; Sakuraba S; Kono H
J Comput Chem; 2014 Jan; 35(1):39-50. PubMed ID: 24166005
[TBL] [Abstract][Full Text] [Related]
5. Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others.
Kamiya N; Yonezawa Y; Nakamura H; Higo J
Proteins; 2008 Jan; 70(1):41-53. PubMed ID: 17636570
[TBL] [Abstract][Full Text] [Related]
6. Multicanonical ab inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment.
Jono R; Watanabe Y; Shimizu K; Terada T
J Comput Chem; 2010 Apr; 31(6):1168-75. PubMed ID: 19847783
[TBL] [Abstract][Full Text] [Related]
7. Free energy landscapes of peptides by enhanced conformational sampling.
Nakajima N; Higo J; Kidera A; Nakamura H
J Mol Biol; 2000 Feb; 296(1):197-216. PubMed ID: 10656827
[TBL] [Abstract][Full Text] [Related]
8. Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.
Okumura H
J Chem Phys; 2008 Sep; 129(12):124116. PubMed ID: 19045015
[TBL] [Abstract][Full Text] [Related]
9. Optimization of partial multicanonical molecular dynamics simulations applied to an alanine dipeptide in explicit water solvent.
Okumura H
Phys Chem Chem Phys; 2011 Jan; 13(1):114-26. PubMed ID: 21038036
[TBL] [Abstract][Full Text] [Related]
10. Calibration of force-field dependency in free energy landscapes of peptide conformations by quantum chemical calculations.
Ono S; Kuroda M; Higo J; Nakajima N; Nakamura H
J Comput Chem; 2002 Mar; 23(4):470-6. PubMed ID: 11908083
[TBL] [Abstract][Full Text] [Related]
11. Dynamic Docking Using Multicanonical Molecular Dynamics: Simulating Complex Formation at the Atomistic Level.
Bekker GJ; Kamiya N
Methods Mol Biol; 2021; 2266():187-202. PubMed ID: 33759128
[TBL] [Abstract][Full Text] [Related]
12. 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]
13. Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.
Higo J; Umezawa K
Adv Exp Med Biol; 2014; 805():331-51. PubMed ID: 24446368
[TBL] [Abstract][Full Text] [Related]
14. Metadynamics as a tool for mapping the conformational and free-energy space of peptides--the alanine dipeptide case study.
Vymetal J; Vondrásek J
J Phys Chem B; 2010 Apr; 114(16):5632-42. PubMed ID: 20361773
[TBL] [Abstract][Full Text] [Related]
15. Communication: Microsecond peptide dynamics from nanosecond trajectories: a Langevin approach.
Rzepiela AJ; Schaudinnus N; Buchenberg S; Hegger R; Stock G
J Chem Phys; 2014 Dec; 141(24):241102. PubMed ID: 25554123
[TBL] [Abstract][Full Text] [Related]
16. Folding free-energy landscape of a 10-residue mini-protein, chignolin.
Satoh D; Shimizu K; Nakamura S; Terada T
FEBS Lett; 2006 Jun; 580(14):3422-6. PubMed ID: 16709409
[TBL] [Abstract][Full Text] [Related]
17. Enhanced sampling algorithms.
Mitsutake A; Mori Y; Okamoto Y
Methods Mol Biol; 2013; 924():153-95. PubMed ID: 23034749
[TBL] [Abstract][Full Text] [Related]
18. Comparative characterization of short monomeric polyglutamine peptides by replica exchange molecular dynamics simulation.
Nakano M; Watanabe H; Rothstein SM; Tanaka S
J Phys Chem B; 2010 May; 114(20):7056-61. PubMed ID: 20441177
[TBL] [Abstract][Full Text] [Related]
19. Direct calculations of vibrational absorption and circular dichroism spectra of alanine dipeptide analog in water: quantum mechanical/molecular mechanical molecular dynamics simulations.
Yang S; Cho M
J Chem Phys; 2009 Oct; 131(13):135102. PubMed ID: 19814574
[TBL] [Abstract][Full Text] [Related]
20. Generation of initial trajectories for transition path sampling of chemical reactions with ab initio molecular dynamics.
Rowley CN; Woo TK
J Chem Phys; 2007 Jan; 126(2):024110. PubMed ID: 17228946
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]