Literature DB >> 12198485

Molecular dynamics simulations of biomolecules.

Martin Karplus1, J Andrew McCammon.   

Abstract

Molecular dynamics simulations are important tools for understanding the physical basis of the structure and function of biological macromolecules. The early view of proteins as relatively rigid structures has been replaced by a dynamic model in which the internal motions and resulting conformational changes play an essential role in their function. This review presents a brief description of the origin and early uses of biomolecular simulations. It then outlines some recent studies that illustrate the utility of such simulations and closes with a discussion of their ever-increasing potential for contributing to biology.

Mesh:

Year:  2002        PMID: 12198485     DOI: 10.1038/nsb0902-646

Source DB:  PubMed          Journal:  Nat Struct Biol        ISSN: 1072-8368


  598 in total

1.  Study, by use of coarse-grained models, of the functionally crucial residues and allosteric pathway of anesthetic regulation of the Gloeobacter violaceus ligand-gated ion channel.

Authors:  Xing Yuan Li; Fang Xie; Jing Chao Zhang; Ji Guo Su
Journal:  Eur Biophys J       Date:  2014-11-04       Impact factor: 1.733

2.  Polymorphism of the epidermal growth factor receptor extracellular ligand binding domain: the dimer interface depends on domain stabilization.

Authors:  Zhiyong Zhang; Willy Wriggers
Journal:  Biochemistry       Date:  2011-02-18       Impact factor: 3.162

3.  An algebraic spline model of molecular surfaces for energetic computations.

Authors:  Wenqi Zhao; Guoliang Xu; Chandrajit Bajaj
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2011 Nov-Dec       Impact factor: 3.710

4.  Analysis of functional motions in Brownian molecular machines with an efficient block normal mode approach: myosin-II and Ca2+ -ATPase.

Authors:  Guohui Li; Qiang Cui
Journal:  Biophys J       Date:  2004-02       Impact factor: 4.033

5.  Engineering teams up with computer-simulation and visualization tools to probe biomolecular mechanisms.

Authors:  Tamar Schlick
Journal:  Biophys J       Date:  2003-07       Impact factor: 4.033

6.  Multistep mechanism of chloride translocation in a strongly anion-selective porin channel.

Authors:  Ulrich Zachariae; Volkhard Helms; Harald Engelhardt
Journal:  Biophys J       Date:  2003-08       Impact factor: 4.033

7.  Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation.

Authors:  Jianhan Chen; Charles L Brooks; Peter E Wright
Journal:  J Biomol NMR       Date:  2004-07       Impact factor: 2.835

8.  Multiple folding pathways of the SH3 domain.

Authors:  Jose M Borreguero; Feng Ding; Sergey V Buldyrev; H Eugene Stanley; Nikolay V Dokholyan
Journal:  Biophys J       Date:  2004-07       Impact factor: 4.033

9.  Study of peptide fingerprints of parasite proteins and drug-DNA interactions with Markov-Mean-Energy invariants of biopolymer molecular-dynamic lattice networks.

Authors:  Lázaro Guillermo Pérez-Montoto; María Auxiliadora Dea-Ayuela; Francisco J Prado-Prado; Francisco Bolas-Fernández; Florencio M Ubeira; Humberto González-Díaz
Journal:  Polymer (Guildf)       Date:  2009-06-03       Impact factor: 4.430

10.  Network visualization of conformational sampling during molecular dynamics simulation.

Authors:  Logan S Ahlstrom; Joseph Lee Baker; Kent Ehrlich; Zachary T Campbell; Sunita Patel; Ivan I Vorontsov; Florence Tama; Osamu Miyashita
Journal:  J Mol Graph Model       Date:  2013-10-16       Impact factor: 2.518

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