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There are 21461 results for: content related to: A convective replica-exchange method for sampling new energy basins

  1. Asynchronous replica exchange for molecular simulations

    Journal of Computational Chemistry

    Volume 29, Issue 5, 15 April 2008, Pages: 788–794, Emilio Gallicchio, Ronald M. Levy and Manish Parashar

    Version of Record online : 17 SEP 2007, DOI: 10.1002/jcc.20839

  2. Generalized-ensemble algorithms for molecular simulations of biopolymers

    Peptide Science

    Volume 60, Issue 2, 2001, Pages: 96–123, Ayori Mitsutake, Yuji Sugita and Yuko Okamoto

    Version of Record online : 6 JUL 2001, DOI: 10.1002/1097-0282(2001)60:2<96::AID-BIP1007>3.0.CO;2-F

  3. Two-dimensional replica-exchange method for predicting protein–ligand binding structures

    Journal of Computational Chemistry

    Volume 34, Issue 30, 15 November 2013, Pages: 2601–2614, Hironori Kokubo, Toshimasa Tanaka and Yuko Okamoto

    Version of Record online : 4 SEP 2013, DOI: 10.1002/jcc.23427

  4. Replica state exchange metadynamics for improving the convergence of free energy estimates

    Journal of Computational Chemistry

    Volume 36, Issue 19, July 15, 2015, Pages: 1446–1455, Raimondas Galvelis and Yuji Sugita

    Version of Record online : 19 MAY 2015, DOI: 10.1002/jcc.23945

  5. Protein structure prediction with the UNRES force-field using Replica-Exchange Monte Carlo-with-Minimization; Comparison with MCM, CSA, and CFMC

    Journal of Computational Chemistry

    Volume 26, Issue 14, 15 November 2005, Pages: 1472–1486, Marian Nanias, Maurizio Chinchio, Stanisław Ołdziej, Cezary Czaplewski and Harold A. Scheraga

    Version of Record online : 8 AUG 2005, DOI: 10.1002/jcc.20286

  6. Coulomb replica-exchange method: Handling electrostatic attractive and repulsive forces for biomolecules

    Journal of Computational Chemistry

    Volume 34, Issue 8, 30 March 2013, Pages: 622–639, Satoru G. Itoh and Hisashi Okumura

    Version of Record online : 29 NOV 2012, DOI: 10.1002/jcc.23167

  7. REIN: Replica-exchange INterface for simulating protein dynamics and function

    International Journal of Quantum Chemistry

    Volume 115, Issue 5, March 5, 2015, Pages: 325–332, Naoyuki Miyashita, Suyong Re and Yuji Sugita

    Version of Record online : 12 SEP 2014, DOI: 10.1002/qua.24785

  8. Multiple-Replica Exchange with Information Retrieval

    ChemPhysChem

    Volume 9, Issue 16, November 10, 2008, Pages: 2332–2339, Manuel Athènes and Florent Calvo

    Version of Record online : 16 OCT 2008, DOI: 10.1002/cphc.200800427

  9. Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

    Proteins: Structure, Function, and Bioinformatics

    Volume 46, Issue 2, 1 February 2002, Pages: 225–234, K.Y. Sanbonmatsu and A.E. García

    Version of Record online : 7 DEC 2001, DOI: 10.1002/prot.1167

  10. Development and application of enhanced sampling techniques to simulate the long-time scale dynamics of biomolecular systems

    International Journal of Quantum Chemistry

    Volume 112, Issue 1, January 2012, Pages: 33–43, Justin Spiriti, Hiqmet Kamberaj and Arjan Van Der Vaart

    Version of Record online : 23 MAY 2011, DOI: 10.1002/qua.23139

  11. Mechanisms for building autonomically scalable services on cooperatively shared computing platforms

    Software: Practice and Experience

    Volume 44, Issue 10, October 2014, Pages: 1251–1276, Vinit Padhye and Anand Tripathi

    Version of Record online : 11 JUN 2013, DOI: 10.1002/spe.2206

  12. Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations

    Proteins: Structure, Function, and Bioinformatics

    Volume 82, Issue 12, December 2014, Pages: 3410–3419, Katja Ostermeir and Martin Zacharias

    Version of Record online : 9 OCT 2014, DOI: 10.1002/prot.24695

  13. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential

    Proteins: Structure, Function, and Bioinformatics

    Volume 66, Issue 3, 15 February 2007, Pages: 697–706, Srinivasaraghavan Kannan and Martin Zacharias

    Version of Record online : 21 NOV 2006, DOI: 10.1002/prot.21258

  14. Walking freely in the energy and temperature space by the modified replica exchange molecular dynamics method

    Journal of Computational Chemistry

    Volume 37, Issue 17, June 30, 2016, Pages: 1565–1575, Changjun Chen and Yanzhao Huang

    Version of Record online : 5 APR 2016, DOI: 10.1002/jcc.24371

  15. Folding simulations of Trp-cage mini protein in explicit solvent using biasing potential replica-exchange molecular dynamics simulations

    Proteins: Structure, Function, and Bioinformatics

    Volume 76, Issue 2, 1 August 2009, Pages: 448–460, Srinivasaraghavan Kannan and Martin Zacharias

    Version of Record online : 23 DEC 2008, DOI: 10.1002/prot.22359

  16. You have free access to this content
    ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level

    Journal of Computational Chemistry

    Volume 31, Issue 5, 15 April 2010, Pages: 1106–1116, Simone Marsili, Giorgio Federico Signorini, Riccardo Chelli, Massimo Marchi and Piero Procacci

    Version of Record online : 12 OCT 2009, DOI: 10.1002/jcc.21388

  17. Characterization of conformational equilibria through Hamiltonian and temperature replica-exchange simulations: Assessing entropic and environmental effects

    Journal of Computational Chemistry

    Volume 28, Issue 10, 30 July 2007, Pages: 1634–1647, José D. Faraldo-Gómez and Benoît Roux

    Version of Record online : 6 MAR 2007, DOI: 10.1002/jcc.20652

  18. Exploring the energy landscape of a β hairpin in explicit solvent

    Proteins: Structure, Function, and Bioinformatics

    Volume 42, Issue 3, 15 February 2001, Pages: 345–354, Angel E. García and Kevin Y. Sanbonmatsu

    Version of Record online : 18 DEC 2000, DOI: 10.1002/1097-0134(20010215)42:3<345::AID-PROT50>3.0.CO;2-H

  19. pH replica-exchange method based on discrete protonation states

    Proteins: Structure, Function, and Bioinformatics

    Volume 79, Issue 12, December 2011, Pages: 3420–3436, Satoru G. Itoh, Ana Damjanović and Bernard R. Brooks

    Version of Record online : 15 OCT 2011, DOI: 10.1002/prot.23176

  20. You have full text access to this OnlineOpen article
    GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 5, Issue 4, July/August 2015, Pages: 310–323, Jaewoon Jung, Takaharu Mori, Chigusa Kobayashi, Yasuhiro Matsunaga, Takao Yoda, Michael Feig and Yuji Sugita

    Version of Record online : 7 MAY 2015, DOI: 10.1002/wcms.1220