Literature DB >> 24492203

Theoretical frameworks for multiscale modeling and simulation.

Huan-Xiang Zhou1.   

Abstract

Biomolecular systems have been modeled at a variety of scales, ranging from explicit treatment of electrons and nuclei to continuum description of bulk deformation or velocity. Many challenges of interfacing between scales have been overcome. Multiple models at different scales have been used to study the same system or calculate the same property (e.g., channel conductance). Accurate modeling of biochemical processes under in vivo conditions and the bridging of molecular and subcellular scales will likely soon become reality.
Copyright © 2014 Elsevier Ltd. All rights reserved.

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Year:  2014        PMID: 24492203      PMCID: PMC4040314          DOI: 10.1016/j.sbi.2014.01.004

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


  81 in total

1.  Peptide aggregation and pore formation in a lipid bilayer: a combined coarse-grained and all atom molecular dynamics study.

Authors:  Lea Thøgersen; Birgit Schiøtt; Thomas Vosegaard; Niels Chr Nielsen; Emad Tajkhorshid
Journal:  Biophys J       Date:  2008-08-01       Impact factor: 4.033

2.  Simulation of ion transport through an N-acetylneuraminic acid-inducible membrane channel: from understanding to engineering.

Authors:  Jing Lu; Niraj Modi; Ulrich Kleinekathöfer
Journal:  J Phys Chem B       Date:  2013-11-14       Impact factor: 2.991

3.  Molecular and subcellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice.

Authors:  Peter M Kekenes-Huskey; Tao Liao; Andrew K Gillette; Johan E Hake; Yongjie Zhang; Anushka P Michailova; Andrew D McCulloch; J Andrew McCammon
Journal:  Biophys J       Date:  2013-11-05       Impact factor: 4.033

4.  Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding site.

Authors:  Huan-Xiang Zhou
Journal:  J Chem Phys       Date:  2011-04-07       Impact factor: 3.488

5.  Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel.

Authors:  Martin B Ulmschneider; Claire Bagnéris; Emily C McCusker; Paul G Decaen; Markus Delling; David E Clapham; Jakob P Ulmschneider; B A Wallace
Journal:  Proc Natl Acad Sci U S A       Date:  2013-03-29       Impact factor: 11.205

6.  Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel.

Authors:  Qiang Shi; Sergei Izvekov; Gregory A Voth
Journal:  J Phys Chem B       Date:  2006-08-10       Impact factor: 2.991

7.  Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin.

Authors:  O Schaad; H X Zhou; A Szabo; W A Eaton; E R Henry
Journal:  Proc Natl Acad Sci U S A       Date:  1993-10-15       Impact factor: 11.205

8.  The electrostatics of VDAC: implications for selectivity and gating.

Authors:  Om P Choudhary; Rachna Ujwal; William Kowallis; Rob Coalson; Jeff Abramson; Michael Grabe
Journal:  J Mol Biol       Date:  2009-12-11       Impact factor: 5.469

9.  Proton transport behavior through the influenza A M2 channel: insights from molecular simulation.

Authors:  Hanning Chen; Yujie Wu; Gregory A Voth
Journal:  Biophys J       Date:  2007-08-10       Impact factor: 4.033

10.  PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations.

Authors:  Phillip J Stansfeld; Richard Hopkinson; Frances M Ashcroft; Mark S P Sansom
Journal:  Biochemistry       Date:  2009-11-24       Impact factor: 3.162

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  11 in total

1.  Predicting 3D Structure, Flexibility, and Stability of RNA Hairpins in Monovalent and Divalent Ion Solutions.

Authors:  Ya-Zhou Shi; Lei Jin; Feng-Hua Wang; Xiao-Long Zhu; Zhi-Jie Tan
Journal:  Biophys J       Date:  2015-12-15       Impact factor: 4.033

Review 2.  Molecular dynamics simulations of large macromolecular complexes.

Authors:  Juan R Perilla; Boon Chong Goh; C Keith Cassidy; Bo Liu; Rafael C Bernardi; Till Rudack; Hang Yu; Zhe Wu; Klaus Schulten
Journal:  Curr Opin Struct Biol       Date:  2015-04-04       Impact factor: 6.809

3.  Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions.

Authors:  Lei Jin; Ya-Zhou Shi; Chen-Jie Feng; Ya-Lan Tan; Zhi-Jie Tan
Journal:  Biophys J       Date:  2018-08-30       Impact factor: 4.033

Review 4.  Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

Authors:  Tatiana Maximova; Ryan Moffatt; Buyong Ma; Ruth Nussinov; Amarda Shehu
Journal:  PLoS Comput Biol       Date:  2016-04-28       Impact factor: 4.475

Review 5.  Adaptive resolution simulations of biomolecular systems.

Authors:  Julija Zavadlav; Staš Bevc; Matej Praprotnik
Journal:  Eur Biophys J       Date:  2017-09-13       Impact factor: 1.733

Review 6.  Recent advances in transferable coarse-grained modeling of proteins.

Authors:  Parimal Kar; Michael Feig
Journal:  Adv Protein Chem Struct Biol       Date:  2014-08-24       Impact factor: 3.507

Review 7.  The chromatin fiber: multiscale problems and approaches.

Authors:  Gungor Ozer; Antoni Luque; Tamar Schlick
Journal:  Curr Opin Struct Biol       Date:  2015-06-05       Impact factor: 6.809

8.  Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

Authors:  Lin Shen; Weitao Yang
Journal:  J Chem Theory Comput       Date:  2016-03-15       Impact factor: 6.006

Review 9.  Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations.

Authors:  Nina Pastor; Carlos Amero
Journal:  Front Plant Sci       Date:  2015-05-05       Impact factor: 5.753

10.  Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.

Authors:  Ya-Zhou Shi; Lei Jin; Chen-Jie Feng; Ya-Lan Tan; Zhi-Jie Tan
Journal:  PLoS Comput Biol       Date:  2018-06-07       Impact factor: 4.475

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