Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations

Protein Engineering, Design & Selection : PEDS
Andrew M SimmsV Daggett

Abstract

Dynameomics is a project to investigate and catalog the native-state dynamics and thermal unfolding pathways of representatives of all protein folds using solvated molecular dynamics simulations, as described in the preceding paper. Here we introduce the design of the molecular dynamics data warehouse, a scalable, reliable repository that houses simulation data that vastly simplifies management and access. In the succeeding paper, we describe the development of a complementary multidimensional database. A single protein unfolding or native-state simulation can take weeks to months to complete, and produces gigabytes of coordinate and analysis data. Mining information from over 3000 completed simulations is complicated and time-consuming. Even the simplest queries involve writing intricate programs that must be built from low-level file system access primitives and include significant logic to correctly locate and parse data of interest. As a result, programs to answer questions that require data from hundreds of simulations are very difficult to write. Thus, organization and access to simulation data have been major obstacles to the discovery of new knowledge in the Dynameomics project. This repository is used internally and is...Continue Reading

Citations

Sep 15, 2011·Journal of Computer-aided Molecular Design·Laurence Leherte, Daniel P Vercauteren
Feb 19, 2013·Journal of Chemical Information and Modeling·Julien C ThibaultThomas E Cheatham
Dec 3, 2009·Journal of the American Chemical Society·Jason KeyKevin H Gardner
Dec 17, 2008·The Journal of Physical Chemistry. B·Christopher P CalderonDennis D Cox
Aug 21, 2008·Proceedings of the National Academy of Sciences of the United States of America·David A C BeckValerie Daggett
Nov 12, 2010·Bioinformatics·R Dustin SchaefferValerie Daggett
Dec 21, 2010·Database : the Journal of Biological Databases and Curation·Shabana VohraPhilip C Biggin
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Noah C Benson, Valerie Daggett
Feb 4, 2014·Journal of Cheminformatics·Julien C ThibaultThomas E Cheatham
Dec 4, 2012·The Journal of Supercomputing·Andrew M Simms, Valerie Daggett
Jul 14, 2010·Computational Biology and Chemistry·Hyun JooJerry Tsai
Jun 10, 2011·Journal of the American Chemical Society·Charles K Fisher, Collin M Stultz
Jan 5, 2010·Journal of Chemical Theory and Computation·Christopher P Calderon, Karunesh Arora
Sep 18, 2008·Protein Science : a Publication of the Protein Society·Noah C Benson, Valerie Daggett
Feb 1, 2011·Protein Science : a Publication of the Protein Society·Alexander D Scouras, Valerie Daggett
Mar 19, 2014·Protein Science : a Publication of the Protein Society·Eric D MerkleyJoshua N Adkins
Aug 22, 2014·Protein Science : a Publication of the Protein Society·Steven J RysavyValerie Daggett
Apr 20, 2010·Structure·Marc W van der KampValerie Daggett
Jun 11, 2016·Journal of Chemical Information and Modeling·Zahra HeidariThomas E Cheatham
Aug 10, 2016·Protein Engineering, Design & Selection : PEDS·Dennis BromleyValerie Daggett
Jul 1, 2012·International Journal of Wavelets, Multiresolution and Information Processing·Noah C Benson, Valerie Daggett
Dec 1, 2010·Biomolecular Concepts·Amanda L JonssonValerie Daggett
Dec 8, 2009·Journal of Chemical Theory and Computation·Laurence Leherte, Daniel P Vercauteren

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