ArticleNucleic acids research2011
Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method.Journal of chemical theory and computation · 2020Article
- A critical assessment of finite element modeling approach for protein dynamics.Journal of computer-aided molecular design · 2017Article
- In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation.Acta crystallographica. Section D, Biological crystallography · 2015Article
- 3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.Nucleic acids research · 2013Article
- The 2011 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection.Nucleic acids research · 2011Article
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Authors and funding
5 authors.
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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.
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