Literature DB >> 18446283

Normal modes and essential dynamics.

Steven Hayward1, Bert L de Groot.   

Abstract

Normal mode analysis and essential dynamics analysis are powerful methods used for the analysis of collective motions in biomolecules. Their application has led to an appreciation of the importance of protein dynamics in function and the relationship between structure and dynamical behavior. In this chapter, the methods and their implementation are introduced and recent developments such as elastic networks and advanced sampling techniques are described.

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Year:  2008        PMID: 18446283     DOI: 10.1007/978-1-59745-177-2_5

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  32 in total

1.  Distributions of experimental protein structures on coarse-grained free energy landscapes.

Authors:  Kannan Sankar; Jie Liu; Yuan Wang; Robert L Jernigan
Journal:  J Chem Phys       Date:  2015-12-28       Impact factor: 3.488

2.  Molecular mechanisms, thermodynamics, and dissociation kinetics of knob-hole interactions in fibrin.

Authors:  Olga Kononova; Rustem I Litvinov; Artem Zhmurov; Andrey Alekseenko; Chia Ho Cheng; Silvi Agarwal; Kenneth A Marx; John W Weisel; Valeri Barsegov
Journal:  J Biol Chem       Date:  2013-05-28       Impact factor: 5.157

3.  Structural transitions and energy landscape for Cowpea Chlorotic Mottle Virus capsid mechanics from nanomanipulation in vitro and in silico.

Authors:  Olga Kononova; Joost Snijder; Melanie Brasch; Jeroen Cornelissen; Ruxandra I Dima; Kenneth A Marx; Gijs J L Wuite; Wouter H Roos; Valeri Barsegov
Journal:  Biophys J       Date:  2013-10-15       Impact factor: 4.033

Review 4.  Application of NMR and molecular docking in structure-based drug discovery.

Authors:  Jaime L Stark; Robert Powers
Journal:  Top Curr Chem       Date:  2012

5.  Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.

Authors:  Amanda Li; Michael K Gilson
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

6.  Optimal superpositioning of flexible molecule ensembles.

Authors:  Vytautas Gapsys; Bert L de Groot
Journal:  Biophys J       Date:  2013-01-08       Impact factor: 4.033

7.  Comparative modelling unravels the structural features of eukaryotic TCTP implicated in its multifunctional properties: an in silico approach.

Authors:  Rakesh Kumar; Shweta Saran
Journal:  J Mol Model       Date:  2021-01-07       Impact factor: 1.810

8.  Monte Carlo, harmonic approximation, and coarse-graining approaches for enhanced sampling of biomolecular structure.

Authors:  Tamar Schlick
Journal:  F1000 Biol Rep       Date:  2009-06-29

9.  Principal component and clustering analysis on molecular dynamics data of the ribosomal L11·23S subdomain.

Authors:  Antje Wolf; Karl N Kirschner
Journal:  J Mol Model       Date:  2012-09-08       Impact factor: 1.810

10.  Dynamic allostery in the methionine repressor revealed by force distribution analysis.

Authors:  Wolfram Stacklies; Fei Xia; Frauke Gräter
Journal:  PLoS Comput Biol       Date:  2009-11-20       Impact factor: 4.475

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