{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,16]],"date-time":"2026-05-16T19:47:24Z","timestamp":1778960844010,"version":"3.51.4"},"reference-count":8,"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>Motivation: Identifying the location of binding sites on proteins is of fundamental importance for a wide range of applications, including molecular docking, de novo drug design, structure identification and comparison of functional sites. Here we present Erebus, a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules. The identified substructure contains atoms having the same names, belonging to same amino acids and separated by the same distances (within a given tolerance) as the atoms of the query structure. The accuracy of a match is measured by the root-mean-square deviation or by the normal weight with a given variance. Tests show that our approach can reliably locate rigid binding scaffolds of drugs and metal ions.<\/jats:p>\n               <jats:p>Availability and Implementation: We provide this service through a web server at http:\/\/erebus.dokhlab.org.<\/jats:p>\n               <jats:p>Contact: \u00a0dokh@unc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr129","type":"journal-article","created":{"date-parts":[[2011,4,2]],"date-time":"2011-04-02T04:28:44Z","timestamp":1301718524000},"page":"1327-1329","source":"Crossref","is-referenced-by-count":27,"title":["Rigid substructure search"],"prefix":"10.1093","volume":"27","author":[{"given":"David","family":"Shirvanyants","sequence":"first","affiliation":[{"name":"1 Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-7260 and 2Department Chemistry and Biochemistry, University of California at Los Angeles, CA 90095-1569, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anastassia N.","family":"Alexandrova","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-7260 and 2Department Chemistry and Biochemistry, University of California at Los Angeles, CA 90095-1569, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nikolay V.","family":"Dokholyan","sequence":"additional","affiliation":[{"name":"1 Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, NC 27599-7260 and 2Department Chemistry and Biochemistry, University of California at Los Angeles, CA 90095-1569, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2011,4,1]]},"reference":[{"key":"2023012512185681000_B1","doi-asserted-by":"crossref","first-page":"e1000585","DOI":"10.1371\/journal.pcbi.1000585","article-title":"Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure","volume":"5","author":"Capra","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"2023012512185681000_B2","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7155\/jgaa.00014","article-title":"Planar subgraph isomorphism","volume":"3","author":"Eppstein","year":"1999","journal-title":"J. Graph Algorithms Appl."},{"key":"2023012512185681000_B3","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1093\/bioinformatics\/13.6.593","article-title":"SS3D-P2: a three-dimensional substructure search program for protein motifs based on secondary structure elements","volume":"13","author":"Kato","year":"1997","journal-title":"Bioinformatics"},{"key":"2023012512185681000_B4","doi-asserted-by":"crossref","first-page":"1160","DOI":"10.1093\/bioinformatics\/btq100","article-title":"ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment","volume":"26","author":"Konc","year":"2010","journal-title":"Bioinformatics"},{"key":"2023012512185681000_B5","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1093\/bioinformatics\/btm121","article-title":"Searching for three-dimensional secondary structural patterns in proteins with ProSMoS","volume":"23","author":"Shi","year":"2007","journal-title":"Bioinformatics"},{"key":"2023012512185681000_B6","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1186\/1471-2105-11-446","article-title":"Tableau-based protein substructure search using quadratic programming","volume":"11","author":"Stivala","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2023012512185681000_B7","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1145\/321921.321925","article-title":"An algorithm for subgraph isomorphism","volume":"23","author":"Ullmann","year":"1976","journal-title":"JACM"},{"key":"2023012512185681000_B8","doi-asserted-by":"crossref","first-page":"16622","DOI":"10.1073\/pnas.0906146106","article-title":"Fast screening of protein surfaces using geometric invariant fingerprints","volume":"106","author":"Yin","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1327\/48867967\/bioinformatics_27_9_1327.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/9\/1327\/48867967\/bioinformatics_27_9_1327.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T15:11:25Z","timestamp":1674659485000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/9\/1327\/242904"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,4,1]]},"references-count":8,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2011,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr129","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":[[2011,4,1]]}}}