{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,5]],"date-time":"2026-06-05T07:48:05Z","timestamp":1780645685220,"version":"3.54.1"},"reference-count":46,"publisher":"Public Library of Science (PLoS)","issue":"7","license":[{"start":{"date-parts":[[2007,7,13]],"date-time":"2007-07-13T00:00:00Z","timestamp":1184284800000},"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.0030119","type":"journal-article","created":{"date-parts":[[2007,7,5]],"date-time":"2007-07-05T14:45:30Z","timestamp":1183646730000},"page":"e119","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":218,"title":["Protein\u2013Protein Interaction Hotspots Carved into Sequences"],"prefix":"10.1371","volume":"3","author":[{"given":"Yanay","family":"Ofran","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Burkhard","family":"Rost","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2007,7,13]]},"reference":[{"key":"pcbi-0030119-b001","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1038\/35001009","article-title":"A comprehensive analysis of protein\u2013protein interactions in Saccharomyces cerevisiae.","volume":"403","year":"2000","journal-title":"Nature"},{"key":"pcbi-0030119-b002","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","year":"2002","journal-title":"Nature"},{"key":"pcbi-0030119-b003","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","year":"2002","journal-title":"Nature"},{"key":"pcbi-0030119-b004","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.1126\/science.1090289","article-title":"A protein interaction map of Drosophila melanogaster.","volume":"302","year":"2003","journal-title":"Science"},{"key":"pcbi-0030119-b005","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","year":"2004","journal-title":"Science"},{"key":"pcbi-0030119-b006","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1006\/jmbi.1998.1843","article-title":"Anatomy of hot spots in protein interfaces.","volume":"280","year":"1998","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b007","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/S0959-440X(02)00283-X","article-title":"Unraveling hot spots in binding interfaces: Progress and challenges.","volume":"12","year":"2002","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi-0030119-b008","doi-asserted-by":"crossref","first-page":"648","DOI":"10.1038\/31405","article-title":"Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody.","volume":"393","year":"1998","journal-title":"Nature"},{"key":"pcbi-0030119-b009","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/0076-6879(91)02020-A","article-title":"Systematic mutational analyses of protein\u2013protein interfaces.","volume":"202","year":"1991","journal-title":"Methods Enzymol"},{"key":"pcbi-0030119-b010","doi-asserted-by":"crossref","first-page":"302","DOI":"10.1016\/S1367-5931(00)00206-4","article-title":"Combinatorial alanine-scanning.","volume":"5","year":"2001","journal-title":"Curr Opin Chem Biol"},{"key":"pcbi-0030119-b011","doi-asserted-by":"crossref","first-page":"383","DOI":"10.1126\/science.7529940","article-title":"A hot spot of binding energy in a hormone-receptor interface.","volume":"267","year":"1995","journal-title":"Science"},{"key":"pcbi-0030119-b012","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1093\/bioinformatics\/17.3.284","article-title":"ASEdb: A database of alanine mutations and their effects on the free energy of binding in protein interactions.","volume":"17","year":"2001","journal-title":"Bioinformatics"},{"key":"pcbi-0030119-b013","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1126\/science.1549776","article-title":"Human growth hormone and extracellular domain of its receptor: Crystal structure of the complex.","volume":"255","year":"1992","journal-title":"Science"},{"key":"pcbi-0030119-b014","doi-asserted-by":"crossref","first-page":"R121","DOI":"10.1016\/S1359-0278(96)00056-9","article-title":"Double-mutant cycles: A powerful tool for analyzing protein structure and function.","volume":"1","year":"1996","journal-title":"Fold Des"},{"key":"pcbi-0030119-b015","doi-asserted-by":"crossref","first-page":"1487","DOI":"10.1006\/jmbi.1998.2559","article-title":"Structural response to mutation at a protein\u2013protein interface.","volume":"286","year":"1999","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b016","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1073\/pnas.0407280102","article-title":"The modular architecture of protein\u2013protein binding interfaces.","volume":"102","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030119-b017","doi-asserted-by":"crossref","first-page":"334","DOI":"10.1002\/prot.10085","article-title":"Dissecting protein\u2013protein recognition sites.","volume":"47","year":"2002","journal-title":"Proteins"},{"key":"pcbi-0030119-b018","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1002\/prot.20741","article-title":"Exploiting sequence and structure homologs to identify protein\u2013protein binding sites.","volume":"62","year":"2006","journal-title":"Proteins"},{"key":"pcbi-0030119-b019","doi-asserted-by":"crossref","first-page":"1356","DOI":"10.1046\/j.1432-1033.2002.02767.x","article-title":"Prediction of protein\u2013protein interaction sites in heterocomplexes with neural networks.","volume":"269","year":"2002","journal-title":"Eur J Biochem"},{"key":"pcbi-0030119-b020","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1016\/j.jmb.2003.10.069","article-title":"Identification of protein\u2013protein interaction sites from docking energy landscapes.","volume":"335","year":"2004","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b021","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1002\/prot.20285","article-title":"Optimal docking area: A new method for predicting protein\u2013protein interaction sites.","volume":"58","year":"2005","journal-title":"Proteins"},{"key":"pcbi-0030119-b022","doi-asserted-by":"crossref","first-page":"917","DOI":"10.1006\/jmbi.2000.4092","article-title":"A fast method to predict protein interaction sites from sequences.","volume":"302","year":"2000","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b023","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1002\/1097-0134(20010501)43:2<89::AID-PROT1021>3.0.CO;2-H","article-title":"Residue frequencies and pairing preferences at protein\u2013protein interfaces.","volume":"43","year":"2001","journal-title":"Proteins"},{"key":"pcbi-0030119-b024","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1006\/jmbi.1997.1233","article-title":"Prediction of protein\u2013protein interaction sites using patch analysis.","volume":"272","year":"1997","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b025","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1093\/protein\/gzh020","article-title":"Prediction of protein\u2013protein interaction sites using support vector machines.","volume":"17","year":"2004","journal-title":"Protein Eng Des Sel"},{"key":"pcbi-0030119-b026","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.jmb.2004.02.040","article-title":"ProMate: A structure based prediction program to identify the location of protein\u2013protein binding sites.","volume":"338","year":"2004","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b027","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1016\/S0022-2836(02)01223-8","article-title":"Analysing six types of protein\u2013protein interfaces.","volume":"325","year":"2003","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b028","doi-asserted-by":"crossref","first-page":"e13","DOI":"10.1093\/bioinformatics\/btl303","article-title":"ISIS: Interaction Sites Identified from Sequence.","volume":"23","year":"2007","journal-title":"Bioinformatics"},{"key":"pcbi-0030119-b029","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/S0014-5793(03)00456-3","article-title":"Predicted protein\u2013protein interaction sites from local sequence information.","volume":"544","year":"2003","journal-title":"FEBS Lett"},{"key":"pcbi-0030119-b030","doi-asserted-by":"crossref","first-page":"2496","DOI":"10.1093\/bioinformatics\/bti340","article-title":"An evolution based classifier for prediction of protein interfaces without using protein structures.","volume":"21","year":"2005","journal-title":"Bioinformatics"},{"key":"pcbi-0030119-b031","first-page":"380","article-title":"Predicting protein interaction sites from residue spatial sequence profile and evolution rate.","volume":"580","year":"2005","journal-title":"FEBS Lett"},{"key":"pcbi-0030119-b032","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1016\/j.sbi.2004.02.003","article-title":"Prediction of protein\u2013protein interactions: The CAPRI experiment, its evaluation and implications.","volume":"14","year":"2004","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi-0030119-b033","doi-asserted-by":"crossref","first-page":"7150","DOI":"10.1073\/pnas.87.18.7150","article-title":"Mapping the CD4 binding site for human immunodeficiency virus by alanine-scanning mutagenesis.","volume":"87","year":"1990","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030119-b034","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/S0896-6273(00)80030-6","article-title":"Spatial localization of the K+ channel selectivity filter by mutant cycle-based structure analysis.","volume":"16","year":"1996","journal-title":"Neuron"},{"key":"pcbi-0030119-b035","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1006\/jmbi.1996.0167","article-title":"An evolutionary trace method defines binding surfaces common to protein families.","volume":"257","year":"1996","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b036","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1038\/299371a0","article-title":"The helical hydrophobic moment: A measure of the amphiphilicity of a helix.","volume":"299","year":"1982","journal-title":"Nature"},{"key":"pcbi-0030119-b037","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1016\/j.jmb.2004.10.077","article-title":"Hot regions in protein\u2013protein interactions: The organization and contribution of structurally conserved hot spot residues.","volume":"345","year":"2005","journal-title":"J Mol Biol"},{"key":"pcbi-0030119-b038","first-page":"1027","article-title":"Protein\u2013protein interactions; coupling of structurally conserved residues and of hot spots across interfaces. Implications for docking.","volume":"12","year":"2004","journal-title":"Structure"},{"key":"pcbi-0030119-b039","first-page":"pl2","article-title":"Computational alanine scanning of protein\u2013protein interfaces.","volume":"2004","year":"2004","journal-title":"Sci STKE"},{"key":"pcbi-0030119-b040","doi-asserted-by":"crossref","first-page":"14116","DOI":"10.1073\/pnas.202485799","article-title":"A simple physical model for binding energy hot spots in protein\u2013protein complexes.","volume":"99","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0030119-b041","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped Blast and PSI-Blast: A new generation of protein database search programs.","volume":"25","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0030119-b042","doi-asserted-by":"crossref","unstructured":"RostB 2002 Prediction in 1D: Secondary structure, membrane helices, and accessibility. In: BournePWeissigH Structural bioinformatics Hoboken (New Jersey) Wiley-Liss 649","DOI":"10.1002\/0471721204.ch28"},{"key":"pcbi-0030119-b043","doi-asserted-by":"crossref","first-page":"5896","DOI":"10.1073\/pnas.092147999","article-title":"Interrogating protein interaction networks through structural biology.","volume":"99","year":"2002","journal-title":"Proc Natl Acad Sci"},{"key":"pcbi-0030119-b044","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1110\/ps.3950102","article-title":"Structural similarity to link sequence space: New potential superfamilies and implications for structural genomics.","volume":"11","year":"2002","journal-title":"Protein Sci"},{"key":"pcbi-0030119-b045","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1093\/protein\/13.12.839","article-title":"Evolutionary trace analysis of TGF-beta and related growth factors: Implications for site-directed mutagenesis.","volume":"13","year":"2000","journal-title":"Protein Eng"},{"key":"pcbi-0030119-b046","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1093\/nar\/24.1.201","article-title":"The HSSP database of protein structure\u2013sequence alignments.","volume":"24","year":"1996","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0030119","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,15]],"date-time":"2024-02-15T19:35:19Z","timestamp":1708025719000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0030119"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2007,7,13]]},"references-count":46,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2007,7,13]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0030119","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2007,7,13]]}}}