Dynameomics: a comprehensive database of protein dynamics.
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 (approximately 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.
van der Kamp
Marc W
MW
Department of Bioengineering, University of Washington, Seattle, WA 98195-5013, USA.
Schaeffer
R Dustin
RD
Jonsson
Amanda L
AL
Scouras
Alexander D
AD
Simms
Andrew M
AM
Toofanny
Rudesh D
RD
Benson
Noah C
NC
Anderson
Peter C
PC
Merkley
Eric D
ED
Rysavy
Steven
S
Bromley
Dennis
D
Beck
David A C
DA
Daggett
Valerie
V
D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000379:methods; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D008968:Molecular Conformation; D020641:Polymorphism, Single Nucleotide; D011489:Protein Denaturation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods
D011506:Proteins
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