Literature DB >> 17383173

Multiscale modeling of biomolecular systems: in serial and in parallel.

Gary S Ayton1, Will G Noid, Gregory A Voth.   

Abstract

Considerable progress has been recently achieved in the multiscale modeling of complex biological processes. Multiscale models have now investigated the structure and dynamics of lipid membranes, proteins, peptides and DNA over length and time scales ranging from the atomic to the macroscopic. Serial multiscale methods that parameterize low-resolution coarse-grained models with data from high-resolution models have studied long time or length scale phenomena that cannot be investigated with atomically detailed models. Parallel multiscale methods that directly couple high- and low-resolution models have efficiently explored slow structural transitions and the importance of long-wavelength fluctuations for biological molecules. The success of such models relies upon new theories and methods for constructing accurate multiscale bridges that transfer information between models with different resolutions.

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Year:  2007        PMID: 17383173     DOI: 10.1016/j.sbi.2007.03.004

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  95 in total

1.  Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration.

Authors:  J W Mullinax; W G Noid
Journal:  J Chem Phys       Date:  2010-09-28       Impact factor: 3.488

Review 2.  Model membrane systems and their applications.

Authors:  Yee-Hung M Chan; Steven G Boxer
Journal:  Curr Opin Chem Biol       Date:  2007-11-19       Impact factor: 8.822

3.  The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models.

Authors:  W G Noid; Pu Liu; Yanting Wang; Jhih-Wei Chu; Gary S Ayton; Sergei Izvekov; Hans C Andersen; Gregory A Voth
Journal:  J Chem Phys       Date:  2008-06-28       Impact factor: 3.488

4.  Systematic multiscale parameterization of heterogeneous elastic network models of proteins.

Authors:  Edward Lyman; Jim Pfaendtner; Gregory A Voth
Journal:  Biophys J       Date:  2008-07-25       Impact factor: 4.033

Review 5.  Modeling kinetics of subcellular disposition of chemicals.

Authors:  Stefan Balaz
Journal:  Chem Rev       Date:  2009-05       Impact factor: 60.622

6.  Nanomechanics of collagen microfibrils.

Authors:  Simone Vesentini; Alberto Redaelli; Alfonso Gautieri
Journal:  Muscles Ligaments Tendons J       Date:  2013-05-21

7.  Generic coarse-grained model for protein folding and aggregation.

Authors:  Tristan Bereau; Markus Deserno
Journal:  J Chem Phys       Date:  2009-06-21       Impact factor: 3.488

8.  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

9.  The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures.

Authors:  Vinod Krishna; Will G Noid; Gregory A Voth
Journal:  J Chem Phys       Date:  2009-07-14       Impact factor: 3.488

Review 10.  Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.

Authors:  Ivet Bahar; Timothy R Lezon; Ahmet Bakan; Indira H Shrivastava
Journal:  Chem Rev       Date:  2010-03-10       Impact factor: 60.622

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