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PSCDB: a database for protein structural change upon ligand binding

Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information for understanding the structural ch...

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Autores principales: Amemiya, Takayuki, Koike, Ryotaro, Kidera, Akinori, Ota, Motonori
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245091/
https://www.ncbi.nlm.nih.gov/pubmed/22080505
http://dx.doi.org/10.1093/nar/gkr966
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author Amemiya, Takayuki
Koike, Ryotaro
Kidera, Akinori
Ota, Motonori
author_facet Amemiya, Takayuki
Koike, Ryotaro
Kidera, Akinori
Ota, Motonori
author_sort Amemiya, Takayuki
collection PubMed
description Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information for understanding the structural changes related to protein functions. We gathered 839 protein structural pairs of ligand-free and ligand-bound states from monomeric or homo-dimeric proteins, and constructed the Protein Structural Change DataBase (PSCDB). In the database, we focused on whether the motions were coupled with ligand binding. As a result, the protein structural changes were classified into seven classes, i.e. coupled domain motion (59 structural changes), independent domain motion (70), coupled local motion (125), independent local motion (135), burying ligand motion (104), no significant motion (311) and other type motion (35). PSCDB provides lists of each class. On each entry page, users can view detailed information about the motion, accompanied by a morphing animation of the structural changes. PSCDB is available at http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/.
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spelling pubmed-32450912012-01-10 PSCDB: a database for protein structural change upon ligand binding Amemiya, Takayuki Koike, Ryotaro Kidera, Akinori Ota, Motonori Nucleic Acids Res Articles Proteins are flexible molecules that undergo structural changes to function. The Protein Data Bank contains multiple entries for identical proteins determined under different conditions, e.g. with and without a ligand molecule, which provides important information for understanding the structural changes related to protein functions. We gathered 839 protein structural pairs of ligand-free and ligand-bound states from monomeric or homo-dimeric proteins, and constructed the Protein Structural Change DataBase (PSCDB). In the database, we focused on whether the motions were coupled with ligand binding. As a result, the protein structural changes were classified into seven classes, i.e. coupled domain motion (59 structural changes), independent domain motion (70), coupled local motion (125), independent local motion (135), burying ligand motion (104), no significant motion (311) and other type motion (35). PSCDB provides lists of each class. On each entry page, users can view detailed information about the motion, accompanied by a morphing animation of the structural changes. PSCDB is available at http://idp1.force.cs.is.nagoya-u.ac.jp/pscdb/. Oxford University Press 2012-01 2011-11-10 /pmc/articles/PMC3245091/ /pubmed/22080505 http://dx.doi.org/10.1093/nar/gkr966 Text en © The Author(s) 2011. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Amemiya, Takayuki
Koike, Ryotaro
Kidera, Akinori
Ota, Motonori
PSCDB: a database for protein structural change upon ligand binding
title PSCDB: a database for protein structural change upon ligand binding
title_full PSCDB: a database for protein structural change upon ligand binding
title_fullStr PSCDB: a database for protein structural change upon ligand binding
title_full_unstemmed PSCDB: a database for protein structural change upon ligand binding
title_short PSCDB: a database for protein structural change upon ligand binding
title_sort pscdb: a database for protein structural change upon ligand binding
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245091/
https://www.ncbi.nlm.nih.gov/pubmed/22080505
http://dx.doi.org/10.1093/nar/gkr966
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