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Literature DB >> 12678809

Normal mode analysis with simplified models to investigate the global dynamics of biological systems.

Abstract

Dynamical properties of macromolecules are increasingly being recognized as significantly contributing to biological functions, including catalysis, regulation of activity, etc. In this review, theoretical approaches to the study of dynamics of biological systems and their application are discussed. In particular, simplified models for the normal mode analysis are described.

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Year: 2003 PMID： 12678809 DOI： 10.2174/0929866033479077

Source DB: PubMed Journal: Protein Pept Lett ISSN： 0929-8665 Impact factor: 1.890

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Cited

22 in total

1. A comparative study of motor-protein motions by using a simple elastic-network model.

Authors: Wenjun Zheng; Sebastian Doniach
Journal: Proc Natl Acad Sci U S A Date: 2003-10-29 Impact factor: 11.205

2. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.

Authors: Karsten Suhre; Yves-Henri Sanejouand
Journal: Nucleic Acids Res Date: 2004-07-01 Impact factor: 16.971

3. iGNM: a database of protein functional motions based on Gaussian Network Model.

Authors: Lee-Wei Yang; Xiong Liu; Christopher J Jursa; Mark Holliman; A J Rader; Hassan A Karimi; Ivet Bahar
Journal: Bioinformatics Date: 2005-04-28 Impact factor: 6.937

4. Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism.

Authors: Antoine Taly; Marc Delarue; Thomas Grutter; Michael Nilges; Nicolas Le Novère; Pierre-Jean Corringer; Jean-Pierre Changeux
Journal: Biophys J Date: 2005-04-01 Impact factor: 4.033

5. Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.

Authors: Vojtech Spiwok; Blanka Králová; Igor Tvaroska
Journal: J Mol Model Date: 2008-07-17 Impact factor: 1.810

6. Computational approaches to shed light on molecular mechanisms in biological processes.

Authors: Giorgio Moro; Laura Bonati; Maurizio Bruschi; Ugo Cosentino; Luca De Gioia; Pier Carlo Fantucci; Alessandro Pandini; Elena Papaleo; Demetrio Pitea; Gloria A A Saracino; Giuseppe Zampella
Journal: Theor Chem Acc Date: 2007-05-01 Impact factor: 1.702

Normal mode analysis with simplified models to investigate the global dynamics of biological systems.

1. A comparative study of motor-protein motions by using a simple elastic-network model.

2. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement.

3. iGNM: a database of protein functional motions based on Gaussian Network Model.

4. Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism.

5. Continuous metadynamics in essential coordinates as a tool for free energy modelling of conformational changes.

6. Computational approaches to shed light on molecular mechanisms in biological processes.

7. Calculation of the infrared spectra of proteins.

8. Alzheimer's abeta(1-40) amyloid fibrils feature size-dependent mechanical properties.

9. Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism.

10. An intracellular interaction network regulates conformational transitions in the dopamine transporter.