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PoSSuM: a database of similar protein–ligand binding and putative pockets

Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins f...

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Autores principales: Ito, Jun-Ichi, Tabei, Yasuo, Shimizu, Kana, Tsuda, Koji, Tomii, Kentaro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245044/
https://www.ncbi.nlm.nih.gov/pubmed/22135290
http://dx.doi.org/10.1093/nar/gkr1130
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author Ito, Jun-Ichi
Tabei, Yasuo
Shimizu, Kana
Tsuda, Koji
Tomii, Kentaro
author_facet Ito, Jun-Ichi
Tabei, Yasuo
Shimizu, Kana
Tsuda, Koji
Tomii, Kentaro
author_sort Ito, Jun-Ichi
collection PubMed
description Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Existing databases of ligand-binding sites offer databases of limited scale. For example, SitesBase covers only ∼33 000 known binding sites. Inferring protein function and drug discovery purposes, however, demands a much more comprehensive database including known and putative-binding sites. Using a novel algorithm, we conducted a large-scale all-pairs similarity search for 1.8 million known and potential binding sites in the PDB, and discovered over 14 million similar pairs of binding sites. Here, we present the results as a relational database Pocket Similarity Search using Multiple-sketches (PoSSuM) including all the discovered pairs with annotations of various types. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures, which provides important clues for characterizing protein structures with unclear functions. The PoSSuM database is freely available at http://possum.cbrc.jp/PoSSuM/.
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spelling pubmed-32450442012-01-10 PoSSuM: a database of similar protein–ligand binding and putative pockets Ito, Jun-Ichi Tabei, Yasuo Shimizu, Kana Tsuda, Koji Tomii, Kentaro Nucleic Acids Res Articles Numerous potential ligand-binding sites are available today, along with hundreds of thousands of known binding sites observed in the PDB. Exhaustive similarity search for such vastly numerous binding site pairs is useful to predict protein functions and to enable rapid screening of target proteins for drug design. Existing databases of ligand-binding sites offer databases of limited scale. For example, SitesBase covers only ∼33 000 known binding sites. Inferring protein function and drug discovery purposes, however, demands a much more comprehensive database including known and putative-binding sites. Using a novel algorithm, we conducted a large-scale all-pairs similarity search for 1.8 million known and potential binding sites in the PDB, and discovered over 14 million similar pairs of binding sites. Here, we present the results as a relational database Pocket Similarity Search using Multiple-sketches (PoSSuM) including all the discovered pairs with annotations of various types. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures, which provides important clues for characterizing protein structures with unclear functions. The PoSSuM database is freely available at http://possum.cbrc.jp/PoSSuM/. Oxford University Press 2012-01 2011-11-30 /pmc/articles/PMC3245044/ /pubmed/22135290 http://dx.doi.org/10.1093/nar/gkr1130 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
Ito, Jun-Ichi
Tabei, Yasuo
Shimizu, Kana
Tsuda, Koji
Tomii, Kentaro
PoSSuM: a database of similar protein–ligand binding and putative pockets
title PoSSuM: a database of similar protein–ligand binding and putative pockets
title_full PoSSuM: a database of similar protein–ligand binding and putative pockets
title_fullStr PoSSuM: a database of similar protein–ligand binding and putative pockets
title_full_unstemmed PoSSuM: a database of similar protein–ligand binding and putative pockets
title_short PoSSuM: a database of similar protein–ligand binding and putative pockets
title_sort possum: a database of similar protein–ligand binding and putative pockets
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245044/
https://www.ncbi.nlm.nih.gov/pubmed/22135290
http://dx.doi.org/10.1093/nar/gkr1130
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