A consensus view of protein dynamics

Manuel Rueda; Carles Ferrer-Costa; Tim Meyer; Alberto Pérez; Jordi Camps; Adam Hospital; Josep Lluis Gelpí; Modesto Orozco

doi:10.1073/pnas.0605534104

A consensus view of protein dynamics

Proc Natl Acad Sci U S A. 2007 Jan 16;104(3):796-801. doi: 10.1073/pnas.0605534104. Epub 2007 Jan 10.

Authors

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

Affiliation

¹ Molecular Modelling and Bioinformatics Unit, and Structural Biology Node, Institut de Recerca Biomèdica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology*
Computer Simulation
Crystallography, X-Ray
Models, Molecular
Nuclear Magnetic Resonance, Biomolecular
Protein Binding
Protein Conformation
Protein Folding*
Proteins / chemistry*
Proteins / metabolism*

Substances

Proteins