{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,6]],"date-time":"2026-01-06T02:18:04Z","timestamp":1767665884160},"reference-count":63,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2009,8,28]],"date-time":"2009-08-28T00:00:00Z","timestamp":1251417600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000490","type":"journal-article","created":{"date-parts":[[2009,8,27]],"date-time":"2009-08-27T22:10:15Z","timestamp":1251411015000},"page":"e1000490","update-policy":"http:\/\/dx.doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":65,"title":["Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments"],"prefix":"10.1371","volume":"5","author":[{"given":"Roberto","family":"Mosca","sequence":"first","affiliation":[]},{"given":"Carles","family":"Pons","sequence":"additional","affiliation":[]},{"given":"Juan","family":"Fern\u00e1ndez-Recio","sequence":"additional","affiliation":[]},{"given":"Patrick","family":"Aloy","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,8,28]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/35001009","article-title":"A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae.","volume":"403","author":"P Uetz","year":"2000","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"4569","DOI":"10.1073\/pnas.061034498","article-title":"A comprehensive two-hybrid analysis to explore the yeast protein interactome.","volume":"98","author":"T Ito","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1126\/science.1090289","article-title":"A protein interaction map of Drosophila melanogaster.","volume":"302","author":"L Giot","year":"2003","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1126\/science.1091403","article-title":"A map of the interactome network of the metazoan C. elegans.","volume":"303","author":"S Li","year":"2004","journal-title":"Science"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1038\/nature04532","article-title":"Proteome survey reveals modularity of the yeast cell machinery.","volume":"440","author":"AC Gavin","year":"2006","journal-title":"Nature"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nature04670","article-title":"Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.","volume":"440","author":"NJ Krogan","year":"2006","journal-title":"Nature"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"1173","DOI":"10.1038\/nature04209","article-title":"Towards a proteome-scale map of the human protein-protein interaction network.","volume":"437","author":"JF Rual","year":"2005","journal-title":"Nature"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"957","DOI":"10.1016\/j.cell.2005.08.029","article-title":"A human protein-protein interaction network: a resource for annotating the proteome.","volume":"122","author":"U Stelzl","year":"2005","journal-title":"Cell"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1186\/gb-2006-7-11-120","article-title":"How complete are current yeast and human protein-interaction networks?","volume":"7","author":"GT Hart","year":"2006","journal-title":"Genome Biol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"e2524","DOI":"10.1371\/journal.pone.0002524","article-title":"Contextual specificity in peptide-mediated protein interactions.","volume":"3","author":"A Stein","year":"2008","journal-title":"PLoS ONE"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1959","DOI":"10.1002\/pmic.200700966","article-title":"Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits.","volume":"8","author":"RA Pache","year":"2008","journal-title":"Proteomics"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"989","DOI":"10.1016\/j.jmb.2003.07.006","article-title":"The relationship between sequence and interaction divergence in proteins.","volume":"332","author":"P Aloy","year":"2003","journal-title":"J Mol Biol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"2026","DOI":"10.1126\/science.1092645","article-title":"Structure-based assembly of protein complexes in yeast.","volume":"303","author":"P Aloy","year":"2004","journal-title":"Science"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.sbi.2006.02.002","article-title":"Flexible protein-protein docking.","volume":"16","author":"AM Bonvin","year":"2006","journal-title":"Curr Opin Struct Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1016\/j.sbi.2006.03.003","article-title":"High-resolution protein-protein docking.","volume":"16","author":"JJ Gray","year":"2006","journal-title":"Curr Opin Struct Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.2174\/138920308783565741","article-title":"Recent progress and future directions in protein-protein docking.","volume":"9","author":"DW Ritchie","year":"2008","journal-title":"Curr Protein Pept Sci"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"704","DOI":"10.1002\/prot.21804","article-title":"Docking and scoring protein complexes: CAPRI 3rd Edition.","volume":"69","author":"MF Lensink","year":"2007","journal-title":"Proteins"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1002\/prot.10393","article-title":"Assessment of blind predictions of protein-protein interactions: current status of docking methods.","volume":"52","author":"R Mendez","year":"2003","journal-title":"Proteins"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1002\/prot.20551","article-title":"Assessment of CAPRI predictions in rounds 3\u20135 shows progress in docking procedures.","volume":"60","author":"R Mendez","year":"2005","journal-title":"Proteins"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1006\/jmbi.1997.1203","article-title":"Modelling protein docking using shape complementarity, electrostatics and biochemical information.","volume":"272","author":"HA Gabb","year":"1997","journal-title":"J Mol Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1002\/prot.10389","article-title":"ZDOCK: an initial-stage protein-docking algorithm.","volume":"52","author":"R Chen","year":"2003","journal-title":"Proteins"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1002\/prot.10092","article-title":"Docking unbound proteins using shape complementarity, desolvation, and electrostatics.","volume":"47","author":"R Chen","year":"2002","journal-title":"Proteins"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1002\/prot.21502","article-title":"Integrating statistical pair potentials into protein complex prediction.","volume":"69","author":"J Mintseris","year":"2007","journal-title":"Proteins"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1002\/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6","article-title":"Protein docking using spherical polar Fourier correlations.","volume":"39","author":"DW Ritchie","year":"2000","journal-title":"Proteins"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.1073\/pnas.89.6.2195","article-title":"Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques.","volume":"89","author":"E Katchalski-Katzir","year":"1992","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1110\/ps.19202","article-title":"Soft protein-protein docking in internal coordinates.","volume":"11","author":"J Fernandez-Recio","year":"2002","journal-title":"Protein Sci"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1002\/prot.20575","article-title":"Improving CAPRI predictions: optimized desolvation for rigid-body docking.","volume":"60","author":"J Fernandez-Recio","year":"2005","journal-title":"Proteins"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1002\/prot.10383","article-title":"ICM-DISCO docking by global energy optimization with fully flexible side-chains.","volume":"52","author":"J Fernandez-Recio","year":"2003","journal-title":"Proteins"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1002\/prot.21419","article-title":"pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking.","volume":"68","author":"TM Cheng","year":"2007","journal-title":"Proteins"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1002\/prot.21796","article-title":"Prediction and scoring of docking poses with pyDock.","volume":"69","author":"S Grosdidier","year":"2007","journal-title":"Proteins"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.1021\/ja026939x","article-title":"HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.","volume":"125","author":"C Dominguez","year":"2003","journal-title":"J Am Chem Soc"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1002\/prot.20565","article-title":"Modeling side-chains using molecular dynamics improve recognition of binding region in CAPRI targets.","volume":"60","author":"CJ Camacho","year":"2005","journal-title":"Proteins"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1002\/prot.10394","article-title":"Successful discrimination of protein interactions.","volume":"52","author":"CJ Camacho","year":"2003","journal-title":"Proteins"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/S0022-2836(03)00670-3","article-title":"Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.","volume":"331","author":"JJ Gray","year":"2003","journal-title":"J Mol Biol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1002\/prot.20566","article-title":"ATTRACT: protein-protein docking in CAPRI using a reduced protein model.","volume":"60","author":"M Zacharias","year":"2005","journal-title":"Proteins"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.tibtech.2004.01.006","article-title":"Protein-protein docking: is the glass half-full or half-empty?","volume":"22","author":"S Vajda","year":"2004","journal-title":"Trends Biotechnol"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1002\/prot.20554","article-title":"Classification of protein complexes based on docking difficulty.","volume":"60","author":"S Vajda","year":"2005","journal-title":"Proteins"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1002\/prot.22106","article-title":"Protein-protein docking benchmark version 3.0.","volume":"73","author":"H Hwang","year":"2008","journal-title":"Proteins"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1002\/prot.10334","article-title":"A novel shape complementarity scoring function for protein-protein docking.","volume":"51","author":"R Chen","year":"2003","journal-title":"Proteins"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1006\/jmbi.1996.0859","article-title":"Determination of atomic desolvation energies from the structures of crystallized proteins.","volume":"267","author":"C Zhang","year":"1997","journal-title":"J Mol Biol"},{"key":"ref41","first-page":"160","article-title":"Optimizing protein representations with information theory.","volume":"15","author":"J Mintseris","year":"2004","journal-title":"Genome Inform"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"2001","DOI":"10.1110\/ps.03154503","article-title":"A graph-theory algorithm for rapid protein side-chain prediction.","volume":"12","author":"AA Canutescu","year":"2003","journal-title":"Protein Sci"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"73","DOI":"10.1093\/nar\/26.1.73","article-title":"SGD: Saccharomyces Genome Database.","volume":"26","author":"JM Cherry","year":"1998","journal-title":"Nucleic Acids Res"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank.","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"SF Altschul","year":"1990","journal-title":"J Mol Biol"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"D291","DOI":"10.1093\/nar\/gkj059","article-title":"MODBASE: a database of annotated comparative protein structure models and associated resources.","volume":"34","author":"U Pieper","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"D281","DOI":"10.1093\/nar\/gkm960","article-title":"The Pfam protein families database.","volume":"36","author":"RD Finn","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"D452","DOI":"10.1093\/nar\/gkh052","article-title":"IntAct: an open source molecular interaction database.","volume":"32","author":"H Hermjakob","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"D572","DOI":"10.1093\/nar\/gkl950","article-title":"MINT: the Molecular INTeraction database.","volume":"35","author":"A Chatr-aryamontri","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1186\/1471-2105-9-352","article-title":"Alignment of protein structures in the presence of domain motions.","volume":"9","author":"R Mosca","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1002\/j.1460-2075.1986.tb04288.x","article-title":"The relation between the divergence of sequence and structure in proteins.","volume":"5","author":"C Chothia","year":"1986","journal-title":"Embo J"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"D436","DOI":"10.1093\/nar\/gkj003","article-title":"MPact: the MIPS protein interaction resource on yeast.","volume":"34","author":"U Guldener","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/415141a","article-title":"Functional organization of the yeast proteome by systematic analysis of protein complexes.","volume":"415","author":"AC Gavin","year":"2002","journal-title":"Nature"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/415180a","article-title":"Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.","volume":"415","author":"Y Ho","year":"2002","journal-title":"Nature"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/S1097-2765(04)00003-6","article-title":"High-definition macromolecular composition of yeast RNA-processing complexes.","volume":"13","author":"NJ Krogan","year":"2004","journal-title":"Mol Cell"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1093\/bioinformatics\/btl524","article-title":"Inherent limitations in protein-protein docking procedures.","volume":"23","author":"N Kowalsman","year":"2007","journal-title":"Bioinformatics"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1007\/978-1-60327-058-8_8","article-title":"Protein structure modeling with MODELLER.","volume":"426","author":"N Eswar","year":"2008","journal-title":"Methods Mol Biol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"1317","DOI":"10.1038\/nbt1018","article-title":"Ten thousand interactions for the molecular biologist.","volume":"22","author":"P Aloy","year":"2004","journal-title":"Nat Biotechnol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1002\/prot.10115","article-title":"Principles of docking: An overview of search algorithms and a guide to scoring functions.","volume":"47","author":"I Halperin","year":"2002","journal-title":"Proteins"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1016\/S1097-2765(03)00476-3","article-title":"Assigning function to yeast proteins by integration of technologies.","volume":"12","author":"TR Hazbun","year":"2003","journal-title":"Mol Cell"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1038\/nchembio.119","article-title":"Targeting and tinkering with interaction networks.","volume":"4","author":"RB Russell","year":"2008","journal-title":"Nat Chem Biol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1126\/science.1158684","article-title":"High-quality binary protein interaction map of the yeast interactome network.","volume":"322","author":"H Yu","year":"2008","journal-title":"Science"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1002\/pmic.200600448","article-title":"WI-PHI: a weighted yeast interactome enriched for direct physical interactions.","volume":"7","author":"L Kiemer","year":"2007","journal-title":"Proteomics"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000490","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T07:04:09Z","timestamp":1558508649000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000490"}},"subtitle":[],"editor":[{"given":"Michael","family":"Levitt","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,8,28]]},"references-count":63,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2009,8,28]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000490","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,8,28]]}}}