Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations

@article{citeulike:2984623, abstract = {The goal of Dynameomics is to perform atomistic molecular dynamics (MD) simulations of representative proteins from all known folds in explicit water in their native state and along their thermal unfolding pathways. Here we present 188-fold representatives and their native state simulations and analyses. These 188 targets represent 67\% of all the structures in the Protein Data Bank. The behavior of several specific targets is highlighted to illustrate general properties in the full dataset and to demonstrate the role of MD in understanding protein function and stability. As an example of what can be learned from mining the Dynameomics database, we identified a protein fold with heightened localized dynamics. In one member of this fold family, the motion affects the exposure of its phosphorylation site and acts as an entropy sink to offset another portion of the protein that is relatively immobile in order to present a consistent interface for protein docking. In another member of this family, a polymorphism in the highly mobile region leads to a host of disease phenotypes. We have constructed a web site to provide access to a novel hybrid relational/multidimensional database (described in the succeeding two papers) to view and interrogate simulations of the top 30 targets: http://www.dynameomics.org. The Dynameomics database, currently the largest collection of protein simulations and protein structures in the world, should also be useful for determining the rules governing protein folding and kinetic stability, which should aid in deciphering genomic information and for protein engineering and design. 10.1093/protein/gzn011}, author = {Beck, David A. and Jonsson, Amanda L. and Schaeffer, Dustin R. and Scott, Kathryn A. and Day, Ryan and Toofanny, Rudesh D. and Alonso, Darwin O. and Daggett, Valerie }, citeulike-article-id = {2984623}, doi = {http://dx.doi.org/10.1093/protein/gzn011}, journal = {Protein Engineering, Design and Selection}, keywords = {bioinformatics, database, molecular\_dynamics, protein\_folding}, month = {June}, number = {6}, pages = {353--368}, posted-at = {2008-07-10 11:55:38}, priority = {0}, title = {Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations}, url = {http://dx.doi.org/10.1093/protein/gzn011}, volume = {21}, year = {2008} }

TY - JOUR ID - citeulike:2984623 L3 - citeulike-article-id:2984623 TI - Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations JF - Protein Engineering, Design and Selection VL - 21 IS - 6 SP - 353 EP - 368 N2 - The goal of Dynameomics is to perform atomistic molecular dynamics (MD) simulations of representative proteins from all known folds in explicit water in their native state and along their thermal unfolding pathways. Here we present 188-fold representatives and their native state simulations and analyses. These 188 targets represent 67% of all the structures in the Protein Data Bank. The behavior of several specific targets is highlighted to illustrate general properties in the full dataset and to demonstrate the role of MD in understanding protein function and stability. As an example of what can be learned from mining the Dynameomics database, we identified a protein fold with heightened localized dynamics. In one member of this fold family, the motion affects the exposure of its phosphorylation site and acts as an entropy sink to offset another portion of the protein that is relatively immobile in order to present a consistent interface for protein docking. In another member of this family, a polymorphism in the highly mobile region leads to a host of disease phenotypes. We have constructed a web site to provide access to a novel hybrid relational/multidimensional database (described in the succeeding two papers) to view and interrogate simulations of the top 30 targets: http://www.dynameomics.org. The Dynameomics database, currently the largest collection of protein simulations and protein structures in the world, should also be useful for determining the rules governing protein folding and kinetic stability, which should aid in deciphering genomic information and for protein engineering and design. 10.1093/protein/gzn011 KW - bioinformatics KW - database KW - molecular_dynamics KW - protein_folding AU - Beck, David AU - Jonsson, Amanda AU - Schaeffer, Dustin AU - Scott, Kathryn AU - Day, Ryan AU - Toofanny, Rudesh AU - Alonso, Darwin AU - Daggett, Valerie PY - 2008/06/01/ UR - http://dx.doi.org/10.1093/protein/gzn011 ER -