{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,1]],"date-time":"2025-10-01T15:37:28Z","timestamp":1759333048908},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2007,8,1]],"date-time":"2007-08-01T00:00:00Z","timestamp":1185926400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2007,12]]},"DOI":"10.1186\/1471-2105-8-279","type":"journal-article","created":{"date-parts":[[2007,8,2]],"date-time":"2007-08-02T18:18:26Z","timestamp":1186078706000},"source":"Crossref","is-referenced-by-count":6,"title":["Combination of scoring schemes for protein docking"],"prefix":"10.1186","volume":"8","author":[{"given":"Philipp","family":"Heuser","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dietmar","family":"Schomburg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2007,8,1]]},"reference":[{"issue":"1","key":"1651_CR1","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1002\/1097-0134(20010101)42:1<108::AID-PROT110>3.0.CO;2-O","volume":"42","author":"WS Valdar","year":"2001","unstructured":"Valdar WS, Thornton JM: Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 2001, 42(1):108\u2013124. 10.1002\/1097-0134(20010101)42:1<108::AID-PROT110>3.0.CO;2-O","journal-title":"Proteins"},{"issue":"7","key":"1651_CR2","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1002\/cbic.200300581","volume":"4","author":"P Caffrey","year":"2003","unstructured":"Caffrey P: Conserved amino acid residues correlating with ketoreductase stereospecificity in modular polyketide synthases. Chembiochem 2003, 4(7):654\u2013657. 10.1002\/cbic.200300581","journal-title":"Chembiochem"},{"issue":"5","key":"1651_CR3","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1074\/mcp.M100037-MCP200","volume":"1","author":"CM Deane","year":"2002","unstructured":"Deane CM, Salwinski L, Xenarios I, Eisenberg D: Protein interactions: two methods for assessment of the reliability of high throughput observations. Mol Cell Proteomics 2002, 1(5):349\u2013356. 10.1074\/mcp.M100037-MCP200","journal-title":"Mol Cell Proteomics"},{"issue":"12","key":"1651_CR4","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1016\/S0968-0004(02)02204-1","volume":"27","author":"P Aloy","year":"2002","unstructured":"Aloy P, Russell RB: The third dimension for protein interactions and complexes. Trends Biochem Sci 2002, 27(12):633\u2013638. 10.1016\/S0968-0004(02)02204-1","journal-title":"Trends Biochem Sci"},{"issue":"4","key":"1651_CR5","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1002\/prot.10115","volume":"47","author":"I Halperin","year":"2002","unstructured":"Halperin I, Ma B, Wolfson H, Nussinov R: Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins 2002, 47(4):409\u2013443. 10.1002\/prot.10115","journal-title":"Proteins"},{"key":"1651_CR6","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1186\/1471-2105-7-344","volume":"7","author":"P Heuser","year":"2006","unstructured":"Heuser P, Schomburg D: Optimised amino acid specific weighting factors for unbound protein docking. BMC Bioinformatics 2006, 7: 344. 10.1186\/1471-2105-7-344","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"1651_CR7","doi-asserted-by":"publisher","first-page":"334","DOI":"10.1002\/prot.10085","volume":"47","author":"P Chakrabarti","year":"2002","unstructured":"Chakrabarti P, Janin J: Dissecting protein-protein recognition sites. Proteins 2002, 47(3):334\u2013343. 10.1002\/prot.10085","journal-title":"Proteins"},{"issue":"1","key":"1651_CR8","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1016\/j.jmb.2004.02.040","volume":"338","author":"H Neuvirth","year":"2004","unstructured":"Neuvirth H, Raz R, Schreiber G: ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004, 338(1):181\u2013199. 10.1016\/j.jmb.2004.02.040","journal-title":"J Mol Biol"},{"key":"1651_CR9","volume-title":"Institut f\u00fcr Biochemie","author":"V Grimm","year":"2003","unstructured":"Grimm V: Untersuchung eines wissensbasierten Potentials zur Bewertung von Protein-Protein-Docking-Studien. Institut f\u00fcr Biochemie K\u00f6ln , Universit\u00e4t zu K\u00f6ln; 2003., Doktor: [ http:\/\/kups.ub.uni-koeln.de\/frontdoor.php?source_opus=682 ]"},{"issue":"2","key":"1651_CR10","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1002\/prot.21117","volume":"65","author":"D Kozakov","year":"2006","unstructured":"Kozakov D, Brenke R, Comeau SR, Vajda S: PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 2006, 65(2):392\u2013406. 10.1002\/prot.21117","journal-title":"Proteins"},{"issue":"3","key":"1651_CR11","doi-asserted-by":"publisher","first-page":"364","DOI":"10.1002\/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2-4","volume":"35","author":"G Moont","year":"1999","unstructured":"Moont G, Gabb HA, Sternberg MJ: Use of pair potentials across protein interfaces in screening predicted docked complexes. Proteins 1999, 35(3):364\u2013373. 10.1002\/(SICI)1097-0134(19990515)35:3<364::AID-PROT11>3.0.CO;2-4","journal-title":"Proteins"},{"issue":"2","key":"1651_CR12","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1002\/prot.20560","volume":"60","author":"J Mintseris","year":"2005","unstructured":"Mintseris J, Wiehe K, Pierce B, Anderson R, Chen R, Janin J, Weng Z: Protein-Protein Docking Benchmark 2.0: an update. Proteins 2005, 60(2):214\u2013216. 10.1002\/prot.20560","journal-title":"Proteins"},{"issue":"1","key":"1651_CR13","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1006\/jmbi.1996.0868","volume":"267","author":"F Melo","year":"1997","unstructured":"Melo F, Feytmans E: Novel knowledge-based mean force potential at atomic level. J Mol Biol 1997, 267(1):207\u2013222. 10.1006\/jmbi.1996.0868","journal-title":"J Mol Biol"},{"key":"1651_CR14","volume-title":"R: A language and environment for statistical computing","author":"R Development Core Team","year":"2005","unstructured":"R Development Core Team: R: A language and environment for statistical computing. 2005."},{"key":"1651_CR15","volume-title":"Instutute for Biochemistry\/Cologne University Bioinformatics Center (CUBIC)","author":"O Martin","year":"2006","unstructured":"Martin O: Effcient comprehensive scoring of docked protein complexes - a machine learning approach. Instutute for Biochemistry\/Cologne University Bioinformatics Center (CUBIC) Cologne , University of Cologne; 2006., PhD: [ http:\/\/kups.ub.uni-koeln.de\/frontdoor.php?source_opus=1802 ]"},{"issue":"5","key":"1651_CR16","doi-asserted-by":"publisher","first-page":"2177","DOI":"10.1006\/jmbi.1998.2439","volume":"285","author":"L Lo Conte","year":"1999","unstructured":"Lo Conte L, Chothia C, Janin J: The atomic structure of protein-protein recognition sites. J Mol Biol 1999, 285(5):2177\u20132198. 10.1006\/jmbi.1998.2439","journal-title":"J Mol Biol"},{"key":"1651_CR17","series-title":"Frontiers in molecular biology 31","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1093\/oso\/9780199637614.003.0002","volume-title":"Protein-Protein Recognition","author":"S Jones","year":"2000","unstructured":"Jones S, Thornton JM: Analysis and classification of protein-protein interactions from a structural perspective. Frontiers in molecular biology 31. In Protein-Protein Recognition. Edited by: Kleanthous C. Edited by: Hames B D, Glover D M. Oxford , Oxford University Press; 2000:33\u201359."},{"issue":"3","key":"1651_CR18","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1110\/ps.8.3.603","volume":"8","author":"RM Jackson","year":"1999","unstructured":"Jackson RM: Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: implications for the protein docking problem. Protein Sci 1999, 8(3):603\u2013613.","journal-title":"Protein Sci"},{"issue":"1","key":"1651_CR19","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1006\/jmbi.1996.0634","volume":"264","author":"M Meyer","year":"1996","unstructured":"Meyer M, Wilson P, Schomburg D: Hydrogen bonding and molecular surface shape complementarity as a basis for protein docking. J Mol Biol 1996, 264(1):199\u2013210. 10.1006\/jmbi.1996.0634","journal-title":"J Mol Biol"},{"key":"1651_CR20","volume-title":"Institute for Biochemistry","author":"O Zimmermann","year":"2002","unstructured":"Zimmermann O: Untersuchungen zur Vorhersage der nativen Orientierung von Protein-Komplexen mit Fourier-Korrelationsmethoden. Institute for Biochemistry Cologne , University of Cologne; 2002. [ http:\/\/kups.ub.uni-koeln.de\/frontdoor.php?source_opus=754 ]"},{"issue":"9","key":"1651_CR21","doi-asserted-by":"publisher","first-page":"739","DOI":"10.1093\/protein\/11.9.739","volume":"11","author":"IN Shindyalov","year":"1998","unstructured":"Shindyalov IN, Bourne PE: Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998, 11(9):739\u2013747. 10.1093\/protein\/11.9.739","journal-title":"Protein Eng"},{"key":"1651_CR22","volume-title":"Prentice-Hall, Englewood Cliffs, NJ","author":"JE Dennis","year":"1983","unstructured":"Dennis JE, Schnabel RB: Numerical Methods for Unconstrained Optimization and Nonlinear Equations. Prentice-Hall, Englewood Cliffs, NJ 1983."},{"key":"1651_CR23","doi-asserted-by":"publisher","first-page":"419","DOI":"10.1145\/6187.6192","volume":"11","author":"RB Schnabel Koontz, J.","year":"1985","unstructured":"Schnabel RB Koontz, J. E. and Weiss, B. E.: A modular system of algorithms for unconstrained minimization. ACM Trans Math Software 1985, 11: 419\u2013440. 10.1145\/6187.6192","journal-title":"ACM Trans Math Software"},{"key":"1651_CR24","unstructured":"Heuser P, Martin O: UUPPDD - Unbound Unbound Protein Protein Docking Dataset.[ http:\/\/biotool.uni-koeln.de\/uuppdd\/ ]"},{"issue":"3","key":"1651_CR25","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1006\/jmbi.1996.0859","volume":"267","author":"C Zhang","year":"1997","unstructured":"Zhang C, Vasmatzis G, Cornette JL, DeLisi C: Determination of atomic desolvation energies from the structures of crystallized proteins. J Mol Biol 1997, 267(3):707\u2013726. 10.1006\/jmbi.1996.0859","journal-title":"J Mol Biol"},{"key":"1651_CR26","series-title":"LNI","first-page":"159","volume-title":"Proceedings of the German Conference on Bioinformatics (GCB2005), Hamburg, Germany, October 5-7, 2005","author":"B Huang","year":"2005","unstructured":"Huang B, Schroeder M: Using residue propensities and tightness of fit to improve rigid-body protein-protein docking. LNI. In Proceedings of the German Conference on Bioinformatics (GCB2005), Hamburg, Germany, October 5\u20137, 2005. Volume 71. Edited by: Matthias R, Andrew T, Kurtz S, Willhoeft U. GI; 2005:159\u2013173."},{"issue":"2","key":"1651_CR27","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1093\/protein\/gzh021","volume":"17","author":"KE Gottschalk","year":"2004","unstructured":"Gottschalk KE, Neuvirth H, Schreiber G: A novel method for scoring of docked protein complexes using predicted protein-protein binding sites. Protein Eng Des Sel 2004, 17(2):183\u2013189. 10.1093\/protein\/gzh021","journal-title":"Protein Eng Des Sel"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-279.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-8-279\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-8-279.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,17]],"date-time":"2024-02-17T06:46:41Z","timestamp":1708152401000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-8-279"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2007,8,1]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2007,12]]}},"alternative-id":["1651"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-8-279","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,8,1]]},"article-number":"279"}}