{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T03:45:58Z","timestamp":1793159158552,"version":"4.5.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Background: The sc-PDB database is an annotated archive of druggable binding sites extracted from the Protein Data Bank. It contains all-atoms coordinates for 8166 protein\u2013ligand complexes, chosen for their geometrical and physico-chemical properties. The sc-PDB provides a functional annotation for proteins, a chemical description for ligands and the detailed intermolecular interactions for complexes. The sc-PDB now includes a hierarchical classification of all the binding sites within a functional class.<\/jats:p>\n                  <jats:p>Method: The sc-PDB entries were first clustered according to the protein name indifferent of the species. For each cluster, we identified dissimilar sites (e.g. catalytic and allosteric sites of an enzyme).<\/jats:p>\n                  <jats:p>Scope and applications: The classification of sc-PDB targets by binding site diversity was intended to facilitate chemogenomics approaches to drug design. In ligand-based approaches, it avoids comparing ligands that do not share the same binding site. In structure-based approaches, it permits to quantitatively evaluate the diversity of the binding site definition (variations in size, sequence and\/or structure).<\/jats:p>\n                  <jats:p>Availability: The sc-PDB database is freely available at: http:\/\/bioinfo-pharma.u-strasbg.fr\/scPDB.<\/jats:p>\n                  <jats:p>Contact: \u00a0ekellen@unistra.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr120","type":"journal-article","created":{"date-parts":[[2011,3,13]],"date-time":"2011-03-13T19:38:49Z","timestamp":1300045129000},"page":"1324-1326","source":"Crossref","is-referenced-by-count":108,"title":["sc-PDB: a database for identifying variations and multiplicity of \u2018druggable\u2019 binding sites in proteins"],"prefix":"10.1093","volume":"27","author":[{"given":"Jamel","family":"Meslamani","sequence":"first","affiliation":[{"name":"Structural Chemogenomics Group, Laboratory of Therapeutic Innovation UMR7200 CNRS\/University of Strasbourg, Facult\u00e9 de Pharmacie, 67400 Illkirch, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Didier","family":"Rognan","sequence":"additional","affiliation":[{"name":"Structural Chemogenomics Group, Laboratory of Therapeutic Innovation UMR7200 CNRS\/University of Strasbourg, Facult\u00e9 de Pharmacie, 67400 Illkirch, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther","family":"Kellenberger","sequence":"additional","affiliation":[{"name":"Structural Chemogenomics Group, Laboratory of Therapeutic Innovation UMR7200 CNRS\/University of Strasbourg, Facult\u00e9 de Pharmacie, 67400 Illkirch, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2011,3,12]]},"reference":[{"key":"2023012512184399900_B1","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkp846","article-title":"The Universal Protein Resource (UniProt) in 2010","volume":"38","author":"Apweiler","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2023012512184399900_B2","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkl971","article-title":"The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data","volume":"35","author":"Berman","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023012512184399900_B3","doi-asserted-by":"crossref","first-page":"e12214","DOI":"10.1371\/journal.pone.0012214","article-title":"Binding of protein kinase inhibitors to synapsin I inferred from pair-wise binding site similarity measurements","volume":"5","author":"Defranchi","year":"2010","journal-title":"PLoS ONE"},{"key":"2023012512184399900_B4","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1021\/ci800023x","article-title":"Ranking targets in structure-based virtual screening of three-dimensional protein libraries: methods and problems","volume":"48","author":"Kellenberger","year":"2008","journal-title":"J. Chem. Inf. Model."},{"key":"2023012512184399900_B5","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1021\/ci050372x","article-title":"sc-PDB: an annotated database of druggable binding sites from the protein data bank","volume":"46","author":"Kellenberger","year":"2006","journal-title":"J. Chem. Inf. Model."},{"key":"2023012512184399900_B6","doi-asserted-by":"crossref","first-page":"1755","DOI":"10.1002\/prot.21858","article-title":"A simple and fuzzy method to align and compare druggable ligand-binding sites","volume":"71","author":"Schalon","year":"2008","journal-title":"Proteins"},{"key":"2023012512184399900_B7","doi-asserted-by":"crossref","first-page":"739","DOI":"10.1093\/protein\/11.9.739","article-title":"Protein structure alignment by incremental combinatorial extension (CE) of the optimal path","volume":"11","author":"Shindyalov","year":"1998","journal-title":"Protein Eng."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1324\/48867049\/bioinformatics_27_9_1324.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1324\/48867049\/bioinformatics_27_9_1324.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T10:03:33Z","timestamp":1674641013000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/9\/1324\/242633"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,3,12]]},"references-count":7,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2011,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr120","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,5,1]]},"published":{"date-parts":[[2011,3,12]]}}}