{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T13:00:47Z","timestamp":1772110847095,"version":"3.50.1"},"reference-count":62,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2003,3,28]],"date-time":"2003-03-28T00:00:00Z","timestamp":1048809600000},"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":[[2003,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Shape complementarity is the most basic ingredient of the scoring functions for protein\u2010protein docking. Most grid\u2010based docking algorithms use the total number of grid points at the binding interface to quantify shape complementarity. We have developed a novel Pairwise Shape Complementarity (PSC) function that is conceptually simple and rapid to compute. The favorable component of PSC is the total number of atom pairs between the receptor and the ligand within a distance cutoff. When applied to a benchmark of 49 test cases, PSC consistently ranks near\u2010native structures higher and produces more near\u2010native structures than the traditional grid\u2010based function, and the improvement was seen across all prediction levels and in all categories of the benchmark. Without any post\u2010processing or biological information about the binding site except the complementarity\u2010determining region of antibodies, PSC predicts the complex structure correctly for 6 test cases, and ranks at least one near\u2010native structure in the top 20 predictions for 18 test cases. Our docking program ZDOCK has been parallelized and the average computing time is 4 minutes using sixteen IBM SP3 processors. Both ZDOCK and the benchmark are freely available to academic users (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/zlab.bu.edu\/~rong\/dock\">http:\/\/zlab.bu.edu\/\u223crong\/dock<\/jats:ext-link>). Proteins 2003;51:397\u2013408. \u00a9 2003 Wiley\u2010Liss, Inc.<\/jats:p>","DOI":"10.1002\/prot.10334","type":"journal-article","created":{"date-parts":[[2003,4,10]],"date-time":"2003-04-10T10:02:10Z","timestamp":1049968930000},"page":"397-408","source":"Crossref","is-referenced-by-count":258,"title":["A novel shape complementarity scoring function for protein\u2010protein docking"],"prefix":"10.1002","volume":"51","author":[{"given":"Rong","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhiping","family":"Weng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2003,4,8]]},"reference":[{"key":"e_1_2_6_2_2","doi-asserted-by":"publisher","DOI":"10.1038\/13783"},{"key":"e_1_2_6_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.235"},{"key":"e_1_2_6_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/ng0196-72"},{"key":"e_1_2_6_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0378-1119(99)00511-9"},{"key":"e_1_2_6_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/35051615"},{"key":"e_1_2_6_7_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.287.5450.116"},{"key":"e_1_2_6_8_2","doi-asserted-by":"publisher","DOI":"10.1002\/1097-0061(20000630)17:2<88::AID-YEA20>3.0.CO;2-Y"},{"key":"e_1_2_6_9_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.97.3.1143"},{"key":"e_1_2_6_10_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.080078197"},{"key":"e_1_2_6_11_2","doi-asserted-by":"publisher","DOI":"10.1038\/35001009"},{"key":"e_1_2_6_12_2","doi-asserted-by":"publisher","DOI":"10.1038\/35015709"},{"key":"e_1_2_6_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-7799(01)01846-7"},{"key":"e_1_2_6_14_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(05)80162-9"},{"key":"e_1_2_6_15_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0079-6107(96)00001-6"},{"key":"e_1_2_6_16_2","doi-asserted-by":"publisher","DOI":"10.1016\/S1074-5521(96)90256-2"},{"key":"e_1_2_6_17_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(98)80047-X"},{"key":"e_1_2_6_18_2","first-page":"399","article-title":"Protein\u2010protein docking. Generation and filtering of complexes","volume":"143","author":"Sternberg MJ","year":"2000","journal-title":"Methods Mol Biol"},{"key":"e_1_2_6_19_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(02)00285-3"},{"key":"e_1_2_6_20_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10115"},{"key":"e_1_2_6_21_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(91)90859-5"},{"key":"e_1_2_6_22_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.6.2195"},{"key":"e_1_2_6_23_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(1997)1 <226::AID-PROT31>3.0.CO;2-O"},{"key":"e_1_2_6_24_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.96.15.8477"},{"key":"e_1_2_6_25_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1997.1203"},{"key":"e_1_2_6_26_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1997.1519"},{"key":"e_1_2_6_27_2","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/14.2.105"},{"key":"e_1_2_6_28_2","first-page":"190","volume-title":"Optimization in molecular biology and computational chemistry","author":"Mitchell JC","year":"2000"},{"key":"e_1_2_6_29_2","first-page":"180","volume-title":"Coupled optimization in protein docking","author":"Mitchell JC","year":"1999"},{"key":"e_1_2_6_30_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(19990815)36:3<307::AID-PROT5>3.0.CO;2-R"},{"key":"e_1_2_6_31_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(20000601)39:4<372::AID-PROT100>3.0.CO;2-Q"},{"key":"e_1_2_6_32_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6"},{"key":"e_1_2_6_33_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.1070"},{"key":"e_1_2_6_34_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10092"},{"key":"e_1_2_6_35_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.19202"},{"key":"e_1_2_6_36_2","doi-asserted-by":"publisher","DOI":"10.1093\/protein\/12.4.271"},{"key":"e_1_2_6_37_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0021889883010985"},{"key":"e_1_2_6_38_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.6879170"},{"key":"e_1_2_6_39_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1995.0493"},{"key":"e_1_2_6_40_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(95)80063-8"},{"key":"e_1_2_6_41_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0634"},{"key":"e_1_2_6_42_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(82)90153-X"},{"key":"e_1_2_6_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(91)80222-G"},{"key":"e_1_2_6_44_2","doi-asserted-by":"publisher","DOI":"10.1110\/ps.2830102"},{"key":"e_1_2_6_45_2","article-title":"A protein\u2010protein docking benchmark","author":"Chen R","journal-title":"Proteins"},{"key":"e_1_2_6_46_2","doi-asserted-by":"publisher","DOI":"10.1107\/S0567740872003723"},{"key":"e_1_2_6_47_2","first-page":"179","volume-title":"The molecular replacement method","author":"Lattman EE","year":"1972"},{"key":"e_1_2_6_48_2","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(71)90324-X"},{"key":"e_1_2_6_49_2","doi-asserted-by":"publisher","DOI":"10.1038\/nsb0396-233"},{"key":"e_1_2_6_50_2","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560040613"},{"key":"e_1_2_6_51_2","doi-asserted-by":"publisher","DOI":"10.1007\/BF02337562"},{"key":"e_1_2_6_52_2","doi-asserted-by":"publisher","DOI":"10.1016\/0959-440X(95)80081-6"},{"key":"e_1_2_6_53_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(96)80075-3"},{"key":"e_1_2_6_54_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0114"},{"key":"e_1_2_6_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(97)80029-2"},{"key":"e_1_2_6_56_2","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560060512"},{"key":"e_1_2_6_57_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0161-5890(96)00090-9"},{"key":"e_1_2_6_58_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1097-0134(19990201)34:2<255::AID-PROT10>3.0.CO;2-O"},{"key":"e_1_2_6_59_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1996.0859"},{"key":"e_1_2_6_60_2","doi-asserted-by":"publisher","DOI":"10.1038\/319199a0"},{"key":"e_1_2_6_61_2","doi-asserted-by":"publisher","DOI":"10.1002\/1097-0134(20001001)41:1<47::AID-PROT80>3.0.CO;2-8"},{"key":"e_1_2_6_62_2","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1998.2439"},{"key":"e_1_2_6_63_2","doi-asserted-by":"publisher","DOI":"10.1002\/prot.10085"}],"container-title":["Proteins: Structure, Function, and Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.wiley.com\/onlinelibrary\/tdm\/v1\/articles\/10.1002%2Fprot.10334","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/prot.10334","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,15]],"date-time":"2023-10-15T13:08:23Z","timestamp":1697375303000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/prot.10334"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2003,4,8]]},"references-count":62,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2003,5,15]]}},"alternative-id":["10.1002\/prot.10334"],"URL":"https:\/\/doi.org\/10.1002\/prot.10334","archive":["Portico"],"relation":{},"ISSN":["0887-3585","1097-0134"],"issn-type":[{"value":"0887-3585","type":"print"},{"value":"1097-0134","type":"electronic"}],"subject":[],"published":{"date-parts":[[2003,4,8]]}}}