Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies
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Bathe_Conformational Dynamics.pdf
Size
2.43 MB
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Author(s)
Kim, Do-Nyun
Altschuler, Josiah
Strong, Campbell
McGill, Gael
Bathe, Mark
Date Issued
November 2010
Journal
Nucleic Acids Research
Publisher
Oxford University Press
Citation
Kim, D.-N. et al. “Conformational Dynamics Data Bank: A Database for Conformational Dynamics of Proteins and Supramolecular Protein Assemblies.” Nucleic Acids Research 39.Database (2010) : D451-D455.
Version
Final published version
Abstract
The conformational dynamics data bank (CDDB, http://www.cdyn.org) is a database that aims to provide comprehensive results on the conformational dynamics of high molecular weight proteins and protein assemblies. Analysis is performed using a recently introduced coarse-grained computational approach that is applied to the majority of structures present in the electron microscopy data bank (EMDB). Results include equilibrium thermal fluctuations and elastic strain energy distributions that identify rigid versus flexible protein domains generally, as well as those associated with specific functional transitions, and correlations in molecular motions that identify molecular regions that are highly coupled dynamically, with implications for allosteric mechanisms. A practical web-based search interface enables users to easily collect conformational dynamics data in various formats. The data bank is maintained and updated automatically to include conformational dynamics results for new structural entries as they become available in the EMDB. The CDDB complements static structural information to facilitate the investigation and interpretation of the biological function of proteins and protein assemblies essential to cell function.
MIT Department
Massachusetts Institute of Technology. Department of Biological Engineering
Terms of Use
Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1093/nar/gkq1088
