{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,4]],"date-time":"2026-10-04T12:41:47Z","timestamp":1791117707534,"version":"4.1.0"},"reference-count":26,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2005,6,24]],"date-time":"2005-06-24T00:00:00Z","timestamp":1119571200000},"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":[[2005,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The abundance of oligomeric proteins makes them a frequent target for structure prediction. However, homologous proteins sometimes adopt different oligomerization states, rendering the prediction of structures of whole oligomers beyond the scope of comparative modeling. This obstacle can be overcome by combining comparative modeling of the single subunit of an oligomer with docking techniques, designed for predicting subunit\u2013subunit interfaces. We present here algorithms for predicting the structures of homo\u2010oligomers with C<jats:sub><jats:italic>n<\/jats:italic><\/jats:sub> or D<jats:sub><jats:italic>n<\/jats:italic><\/jats:sub> (<jats:italic>n<\/jats:italic> &gt; 2) symmetry. The prediction procedure includes a symmetry\u2010restricted docking step followed by a C<jats:sub><jats:italic>n<\/jats:italic><\/jats:sub> or D<jats:sub><jats:italic>n<\/jats:italic><\/jats:sub> oligomer\u2010forming step, in which the dimers from the docking step are assembled to oligomers. The procedure is applied to each of the crystallographically independent subunits in 8 C<jats:sub><jats:italic>n<\/jats:italic><\/jats:sub> and 3 D<jats:sub><jats:italic>n<\/jats:italic><\/jats:sub> oligomers, producing very accurate predictions. It is further applied to a single monomer of the tick\u2010borne encephalitis virus coat protein E (Target 10 of the CAPRI experiment). The predicted trimer ranked 30, obtained via rigid\u2010body geometric\u2013hydrophobic docking followed by C<jats:sub><jats:italic>n<\/jats:italic><\/jats:sub> oligomer formation, is very similar to the experimentally observed trimer formed by domain II of this protein. Furthermore, the predicted trimer formed from the separated domain I is also close to the experimental structure. Proteins 2005;60:202\u2013206. \u00a9 2005 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.20558","type":"journal-article","created":{"date-parts":[[2005,6,24]],"date-time":"2005-06-24T22:17:08Z","timestamp":1119651428000},"page":"202-206","source":"Crossref","is-referenced-by-count":34,"title":["Modeling oligomers with C<sub><i>n<\/i><\/sub> or D<sub><i>n<\/i><\/sub> symmetry: Application to CAPRI target 10"],"prefix":"10.1002","volume":"60","author":[{"given":"Alexander","family":"Berchanski","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dadi","family":"Segal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam","family":"Eisenstein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2005,6,24]]},"reference":[{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.biophys.29.1.105"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0304-4165(01)00153-2"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1023\/A:1005528811303"},{"key":"e_1_2_6_5_2","doi-asserted-by":"publisher","DOI":"10.1038\/scientificamerican1178-62"},{"key":"e_1_2_6_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/sj.emboj.7600064"},{"key":"e_1_2_6_7_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0773"},{"key":"e_1_2_6_8_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10480"},{"key":"e_1_2_6_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/375291a0"},{"key":"e_1_2_6_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.6.2195"},{"key":"e_1_2_6_11_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.26002"},{"key":"e_1_2_6_12_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20145"},{"key":"e_1_2_6_13_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"e_1_2_6_14_2","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/10.10.1101"},{"key":"e_1_2_6_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0897-622"},{"key":"e_1_2_6_16_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0332"},{"key":"e_1_2_6_17_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi992645l"},{"key":"e_1_2_6_18_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(01)00190-3"},{"key":"e_1_2_6_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/367338a0"},{"key":"e_1_2_6_20_2","doi-asserted-by":"publisher","DOI":"10.1038\/37670"},{"key":"e_1_2_6_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(03)00184-0"},{"key":"e_1_2_6_22_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi982990v"},{"key":"e_1_2_6_23_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0969-2126(98)00132-4"},{"key":"e_1_2_6_24_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.240463497"},{"key":"e_1_2_6_25_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.1070"},{"key":"e_1_2_6_26_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10381"},{"key":"e_1_2_6_27_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10391"}],"container-title":["Proteins: Structure, Function, and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fprot.20558","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/prot.20558","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,13]],"date-time":"2023-09-13T21:07:34Z","timestamp":1694639254000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.20558"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2005,6,24]]},"references-count":26,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2005,8]]}},"alternative-id":["10.1002\/prot.20558"],"URL":"https:\/\/doi.org\/10.1002\/prot.20558","archive":["Portico"],"relation":{},"ISSN":["0887-3585","1097-0134"],"issn-type":[{"value":"0887-3585","type":"print"},{"value":"1097-0134","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,6,24]]}}}