Dynameomics: A Comprehensive Database of Protein Dynamics

Marc W. van der Kamp, R. Dustin Schaeffer, Amanda L. Jonsson, Alexander D. Scouras, Andrew M. Simms, Rudesh D. Toofanny, Noah C. Benson, Peter C. Anderson, Eric D. Merkley, Steven Rysavy, Dennis Bromley, David A.C. Beck, Valerie Daggett

Research output: Contribution to journalArticle

96 Scopus citations

Abstract

The dynamic behavior of proteins is important for an understanding of their function and folding. We have performed molecular dynamics simulations of the native state and unfolding pathways of over 2000 protein/peptide systems (∼11,000 independent simulations) representing the majority of folds in globular proteins. These data are stored and organized using an innovative database approach, which can be mined to obtain both general and specific information about the dynamics and folding/unfolding of proteins, relevant subsets thereof, and individual proteins. Here we describe the project in general terms and the type of information contained in the database. Then we provide examples of mining the database for information relevant to protein folding, structure building, the effect of single-nucleotide polymorphisms, and drug design. The native state simulation data and corresponding analyses for the 100 most populated metafolds, together with related resources, are publicly accessible through http://www.dynameomics.org.

Original languageEnglish (US)
Pages (from-to)423-435
Number of pages13
JournalStructure
Volume18
Issue number4
DOIs
StatePublished - Mar 1 2010

Keywords

  • Proteins

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

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    van der Kamp, M. W., Schaeffer, R. D., Jonsson, A. L., Scouras, A. D., Simms, A. M., Toofanny, R. D., Benson, N. C., Anderson, P. C., Merkley, E. D., Rysavy, S., Bromley, D., Beck, D. A. C., & Daggett, V. (2010). Dynameomics: A Comprehensive Database of Protein Dynamics. Structure, 18(4), 423-435. https://doi.org/10.1016/j.str.2010.01.012