Literature DB >> 17215349

A consensus view of protein dynamics.

Manuel Rueda1, Carles Ferrer-Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep Lluis Gelpí, Modesto Orozco.   

Abstract

The dynamics of proteins in aqueous solution has been investigated through a massive approach based on "state of the art" molecular dynamics simulations performed for all protein metafolds using the four most popular force fields (OPLS, CHARMM, AMBER, and GROMOS). A detailed analysis of the massive database of trajectories (>1.5 terabytes of data obtained using approximately 50 years of CPU) allowed us to obtain a robust-consensus picture of protein dynamics in aqueous solution.

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Year:  2007        PMID： 17215349      PMCID： PMC1783393          DOI： 10.1073/pnas.0605534104

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  32 in total

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Authors: 
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3.  Contribution of surface salt bridges to protein stability.

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4.  Cooperativity in drug-DNA recognition: a molecular dynamics study.

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5.  Stabilization of proteins by ligand binding: application to drug screening and determination of unfolding energetics.

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Journal:  Biochemistry       Date:  2003-05-06       Impact factor: 3.162

Review 6.  Molecular dynamics simulations of biomolecules.

Authors:  Martin Karplus; J Andrew McCammon
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Review 7.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

8.  A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.

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Journal:  Protein Sci       Date:  2003-10       Impact factor: 6.725

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  72 in total

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Authors:  Jere P Segrest; Martin K Jones; Andrea Catte; Saravana P Thirumuruganandham
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5.  Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation.

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Review 6.  Protein mechanics: a route from structure to function.

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Journal:  J Biosci       Date:  2007-08       Impact factor: 1.826

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Journal:  J Biol Chem       Date:  2009-03-17       Impact factor: 5.157

Review 8.  Genome and proteome annotation: organization, interpretation and integration.

Authors:  Gabrielle A Reeves; David Talavera; Janet M Thornton
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9.  Stretched DNA investigated using molecular-dynamics and quantum-mechanical calculations.

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10.  Effects of familial Alzheimer's disease mutations on the folding nucleation of the amyloid beta-protein.

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