Literature DB >> 14967236

Conformational sampling for the impatient.

Kaihsu Tai1.   

Abstract

Several new methods for sampling conformations of biomolecules have appeared recently. A brief review thereof is presented, with particular emphasis on applications that have been published, and suitability for different kinds of systems. Four methods (namely: RESPA, replica-exchange molecular dynamics, CONCOORD and Gaussian network method) are readily applicable for biomolecular systems.

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Year:  2004        PMID： 14967236     DOI： 10.1016/j.bpc.2003.09.010

Source DB:  PubMed          Journal:  Biophys Chem        ISSN： 0301-4622            Impact factor:   2.352


  15 in total

1.  The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure.

Authors:  Lauren Wickstrom; Asim Okur; Kun Song; Viktor Hornak; Daniel P Raleigh; Carlos L Simmerling
Journal:  J Mol Biol       Date:  2006-05-15       Impact factor: 5.469

2.  Modified replica exchange simulation methods for local structure refinement.

Authors:  Xiaolin Cheng; Guanglei Cui; Viktor Hornak; Carlos Simmerling
Journal:  J Phys Chem B       Date:  2005-04-28       Impact factor: 2.991

3.  Coupling of replica exchange simulations to a non-Boltzmann structure reservoir.

Authors:  Adrian E Roitberg; Asim Okur; Carlos Simmerling
Journal:  J Phys Chem B       Date:  2007-02-15       Impact factor: 2.991

Review 4.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

5.  Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides.

Authors:  Hernán Stamati; Cecilia Clementi; Lydia E Kavraki
Journal:  Proteins       Date:  2010-02-01

6.  Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides.

Authors:  Sairam S Mallajosyula; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2011-08-31       Impact factor: 2.991

Review 7.  Predicting Binding Free Energies: Frontiers and Benchmarks.

Authors:  David L Mobley; Michael K Gilson
Journal:  Annu Rev Biophys       Date:  2017-04-07       Impact factor: 12.981

8.  Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics.

Authors:  Xiongwu Wu; Ana Damjanovic; Bernard R Brooks
Journal:  Adv Chem Phys       Date:  2012-01-31       Impact factor: 1.000

Review 9.  Principles of flexible protein-protein docking.

Authors:  Nelly Andrusier; Efrat Mashiach; Ruth Nussinov; Haim J Wolfson
Journal:  Proteins       Date:  2008-11-01

10.  Folding of Trp-cage mini protein using temperature and biasing potential replica-exchange molecular dynamics simulations.

Authors:  Srinivasaraghavan Kannan; Martin Zacharias
Journal:  Int J Mol Sci       Date:  2009-03-12       Impact factor: 5.923
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