{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T20:24:35Z","timestamp":1758399875767},"reference-count":43,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2005,10,24]],"date-time":"2005-10-24T00:00:00Z","timestamp":1130112000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteins"],"published-print":{"date-parts":[[2005,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Considering the limited success of the most sophisticated docking methods available and the amount of computation required for systematic docking, cataloging all the known interfaces may be an alternative basis for the prediction of protein tertiary and quaternary structures. We classify domain interfaces according to the geometry of domain\u2013domain association. By applying a simple and efficient method called \u201cinterface tag clustering,\u201d more than 4,000 distinct types of domain interfaces are collected from Protein Quaternary Structure Server and Protein Data Bank. Given a pair of interacting domains, we define \u201cface\u201d as the set of interacting residues in each single domain and the pair of interacting faces as an \u201cinterface.\u201d We investigate how the geometry of interfaces relates to a network of interacting protein families, such as how many different binding orientations are possible between two families or whether a family uses distinct surfaces or the same surface when the family has diverse interaction partners from various families. We show there are, on average, 1.2\u20131.9 different types of interfaces between interacting domains and a significant number of family pairs associate in multiple orientations. In general, a family tends to use distinct faces for each partner when the family has diverse interaction partners. Each face is highly specific to its interaction partner and the binding orientation. The relative positions of interface residues are generally well conserved within the same type of interface even between remote homologs. The classification result is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.biotec.tu-dresden.de\/~wkim\/supplement\">http:\/\/www.biotec.tu\u2010dresden.de\/\u223cwkim\/supplement<\/jats:ext-link>. Proteins 2005. \u00a9 2005 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.20693","type":"journal-article","created":{"date-parts":[[2005,10,24]],"date-time":"2005-10-24T22:47:07Z","timestamp":1130194027000},"page":"1075-1088","source":"Crossref","is-referenced-by-count":23,"title":["Survey of the geometric association of domain\u2013domain interfaces"],"prefix":"10.1002","volume":"61","author":[{"given":"Wan Kyu","family":"Kim","sequence":"first","affiliation":[]},{"given":"Jon 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