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There are 18928 results for: content related to: Development and application of enhanced sampling techniques to simulate the long-time scale dynamics of biomolecular systems

  1. Exploiting the potential energy landscape to sample free energy

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 5, Issue 3, May/June 2015, Pages: 273–289, Andrew J. Ballard, Stefano Martiniani, Jacob D. Stevenson, Sandeep Somani and David J. Wales

    Article first published online : 20 MAR 2015, DOI: 10.1002/wcms.1217

  2. Basic ingredients of free energy calculations: A review

    Journal of Computational Chemistry

    Volume 31, Issue 8, June 2010, Pages: 1569–1582, Clara D. Christ, Alan E. Mark and Wilfred F. van Gunsteren

    Article first published online : 23 DEC 2009, DOI: 10.1002/jcc.21450

  3. You have full text access to this OnlineOpen article
    Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach

    ChemPhysChem

    Volume 16, Issue 15, October 26, 2015, Pages: 3233–3241, Dr. Kepa K. Burusco, Dr. Neil J. Bruce, Irfan Alibay and Dr. Richard A. Bryce

    Article first published online : 29 SEP 2015, DOI: 10.1002/cphc.201500524

  4. You have free access to this content
    Beyond kappa distributions: Exploiting Tsallis statistical mechanics in space plasmas

    Journal of Geophysical Research: Space Physics (1978–2012)

    Volume 114, Issue A11, November 2009, G. Livadiotis and D. J. McComas

    Article first published online : 17 NOV 2009, DOI: 10.1029/2009JA014352

  5. CHARMM: The biomolecular simulation program

    Journal of Computational Chemistry

    Volume 30, Issue 10, 30 July 2009, Pages: 1545–1614, B. R. Brooks, C. L. Brooks III, A. D. Mackerell Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York and M. Karplus

    Article first published online : 14 MAY 2009, DOI: 10.1002/jcc.21287

  6. A convective replica-exchange method for sampling new energy basins

    Journal of Computational Chemistry

    Volume 34, Issue 2, 15 January 2013, Pages: 132–140, Yannick G. Spill, Guillaume Bouvier and Michael Nilges

    Article first published online : 7 SEP 2012, DOI: 10.1002/jcc.23113

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    Erratum: Erratum: A convective replica-exchange method for sampling new energy basins

    Vol. 34, Issue 18, 1609, Article first published online: 8 APR 2013

  7. 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

    Article first published online : 19 MAY 2015, DOI: 10.1002/jcc.23945

  8. 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

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

  9. Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design

    Chemical Biology & Drug Design

    Volume 81, Issue 1, January 2013, Pages: 41–49, William Sinko, Steffen Lindert and J. Andrew McCammon

    Article first published online : 17 DEC 2012, DOI: 10.1111/cbdd.12051

  10. 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

    Article first published online : 21 NOV 2006, DOI: 10.1002/prot.21258

  11. QUADRATIC TSALLIS ENTROPY BIAS AND GENERALIZED MAXIMUM ENTROPY MODELS

    Computational Intelligence

    Volume 30, Issue 2, May 2014, Pages: 233–262, Yuexian Hou, Bo Wang, Dawei Song, Xiaochun Cao and Wenjie Li

    Article first published online : 4 JUL 2012, DOI: 10.1111/j.1467-8640.2012.00443.x

  12. Transition state theory with Tsallis statistics

    Journal of Computational Chemistry

    Volume 31, Issue 3, February 2010, Pages: 573–585, Wolfgang Quapp and Alraune Zech

    Article first published online : 15 JUN 2009, DOI: 10.1002/jcc.21349

  13. Electromagnetic fluctuations of the whistler-cyclotron and firehose instabilities in a Maxwellian and Tsallis-kappa-like plasma

    Journal of Geophysical Research: Space Physics

    Volume 120, Issue 5, May 2015, Pages: 3307–3317, Adolfo F. Viñas, Pablo S. Moya, Roberto E. Navarro, J. Alejandro Valdivia, Jaime A. Araneda and Víctor Muñoz

    Article first published online : 15 MAY 2015, DOI: 10.1002/2014JA020554

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    Tsallis distributions of magnetic field strength variations in the heliosphere: 5 to 90 AU

    Journal of Geophysical Research: Space Physics (1978–2012)

    Volume 112, Issue A7, July 2007, L. F. Burlaga, A. F-Viñas and C. Wang

    Article first published online : 7 JUL 2007, DOI: 10.1029/2006JA012213

  15. 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

    Article first published online : 12 SEP 2014, DOI: 10.1002/qua.24785

  16. How hot? Systematic convergence of the replica exchange method using multiple reservoirs

    Journal of Computational Chemistry

    Volume 31, Issue 3, February 2010, Pages: 620–627, Jory Z. Ruscio, Nicolas L. Fawzi and Teresa Head-Gordon

    Article first published online : 24 JUN 2009, DOI: 10.1002/jcc.21355

  17. 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

    Article first published online : 23 DEC 2008, DOI: 10.1002/prot.22359

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    Multiscale structure of the magnetic field and speed at 1 AU during the declining phase of solar cycle 23 described by a generalized Tsallis probability distribution function

    Journal of Geophysical Research: Space Physics (1978–2012)

    Volume 109, Issue A12, December 2004, L. F. Burlaga and A. F.-Viñas

    Article first published online : 21 DEC 2004, DOI: 10.1029/2004JA010763

  19. Position and momentum information-theoretic measures of the pseudoharmonic potential

    International Journal of Quantum Chemistry

    Volume 115, Issue 21, November 5, 2015, Pages: 1543–1552, W. A. Yahya, K. J. Oyewumi and K. D. Sen

    Article first published online : 22 JUL 2015, DOI: 10.1002/qua.24971

  20. Insights into the binding of intrinsically disordered proteins from molecular dynamics simulation

    Wiley Interdisciplinary Reviews: Computational Molecular Science

    Volume 4, Issue 3, May/June 2014, Pages: 182–198, Christopher M. Baker and Robert B. Best

    Article first published online : 27 AUG 2013, DOI: 10.1002/wcms.1167