TY - JOUR
T1 - Dynameomics
T2 - A Comprehensive Database of Protein Dynamics
AU - van der Kamp, Marc W.
AU - Schaeffer, R. Dustin
AU - Jonsson, Amanda L.
AU - Scouras, Alexander D.
AU - Simms, Andrew M.
AU - Toofanny, Rudesh D.
AU - Benson, Noah C.
AU - Anderson, Peter C.
AU - Merkley, Eric D.
AU - Rysavy, Steven
AU - Bromley, Dennis
AU - Beck, David A.C.
AU - Daggett, Valerie
N1 - Funding Information:
We are grateful for support from Microsoft for development of our database. The simulations for Dynameomics were performed using computer time through the DOE Office of Biological Research as provided by the National Energy Research Scientific Computing Center, which is supported by the Office of Science of the U.S. Department of Energy under contract DE-AC02-05CH11231. We are also grateful for financial support provided by the National Institutes of Health (GM50789 to V.D. and TG 3 T15 LM007442-04S1 to P.C.A., N.C.B., A.S., D.B., and S.R.).
PY - 2010/3
Y1 - 2010/3
N2 - 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.
AB - 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.
KW - Proteins
UR - http://www.scopus.com/inward/record.url?scp=77951680969&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=77951680969&partnerID=8YFLogxK
U2 - 10.1016/j.str.2010.01.012
DO - 10.1016/j.str.2010.01.012
M3 - Article
C2 - 20399180
AN - SCOPUS:77951680969
SN - 0969-2126
VL - 18
SP - 423
EP - 435
JO - Structure
JF - Structure
IS - 4
ER -