Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies
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...
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| Format: | Article |
| Language: | en_US |
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Oxford University Press
2011
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| Online Access: | http://hdl.handle.net/1721.1/66249 https://orcid.org/0000-0002-6199-6855 |
| _version_ | 1826195234421211136 |
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| author | Kim, Do-Nyun Altschuler, Josiah Strong, Campbell McGill, Gael Bathe, Mark |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Kim, Do-Nyun Altschuler, Josiah Strong, Campbell McGill, Gael Bathe, Mark |
| author_sort | Kim, Do-Nyun |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T10:09:31Z |
| format | Article |
| id | mit-1721.1/66249 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:09:31Z |
| publishDate | 2011 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | mit-1721.1/662492022-09-30T19:16:21Z Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies Kim, Do-Nyun Altschuler, Josiah Strong, Campbell McGill, Gael Bathe, Mark Massachusetts Institute of Technology. Department of Biological Engineering Bathe, Mark Kim, Do-Nyun Bathe, Mark 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. 2011-10-13T17:51:07Z 2011-10-13T17:51:07Z 2010-11 2010-10 Article http://purl.org/eprint/type/JournalArticle 0305-1048 1362-4962 http://hdl.handle.net/1721.1/66249 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. 21051356 https://orcid.org/0000-0002-6199-6855 en_US http://dx.doi.org/10.1093/nar/gkq1088 Nucleic Acids Research Creative Commons Attribution http://creativecommons.org/licenses/by/2.5/ application/pdf Oxford University Press Nucleic Acids Research |
| spellingShingle | Kim, Do-Nyun Altschuler, Josiah Strong, Campbell McGill, Gael Bathe, Mark Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies |
| title | Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies |
| title_full | Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies |
| title_fullStr | Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies |
| title_full_unstemmed | Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies |
| title_short | Conformational dynamics data bank: a database for conformational proteins and supramolecular protein assemblies |
| title_sort | conformational dynamics data bank a database for conformational proteins and supramolecular protein assemblies |
| url | http://hdl.handle.net/1721.1/66249 https://orcid.org/0000-0002-6199-6855 |
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