{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T03:05:15Z","timestamp":1780110315588,"version":"3.54.0"},"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2005,8,12]],"date-time":"2005-08-12T00:00:00Z","timestamp":1123804800000},"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.0010026","type":"journal-article","created":{"date-parts":[[2005,8,10]],"date-time":"2005-08-10T18:15:30Z","timestamp":1123697730000},"page":"e26","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":36,"title":["Comparative Genomics and Disorder Prediction Identify Biologically Relevant SH3 Protein Interactions"],"prefix":"10.1371","volume":"1","author":[{"given":"Pedro","family":"Beltrao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Serrano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2005,8,12]]},"reference":[{"key":"pcbi-0010026-b01","first-page":"RESEARCH0034","article-title":"Functional associations of proteins in entire genomes by means of exhaustive detection of gene fusions.","volume":"2","year":"2001","journal-title":"Genome Biol"},{"key":"pcbi-0010026-b02","doi-asserted-by":"crossref","first-page":"751","DOI":"10.1126\/science.285.5428.751","article-title":"Detecting protein function and protein\u2013protein interactions from genome sequences.","volume":"285","year":"1999","journal-title":"Science"},{"key":"pcbi-0010026-b03","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1016\/S0968-0004(98)01274-2","article-title":"Conservation of gene order: A fingerprint of proteins that physically interact.","volume":"23","year":"1998","journal-title":"Trends Biochem Sci"},{"key":"pcbi-0010026-b04","doi-asserted-by":"crossref","first-page":"4285","DOI":"10.1073\/pnas.96.8.4285","article-title":"Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles.","volume":"96","year":"1999","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0010026-b05","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1089\/omi.1.1998.3.199","article-title":"Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes.","volume":"3","year":"1998","journal-title":"Microb Comp Genomics"},{"key":"pcbi-0010026-b06","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1006\/jmbi.2000.3732","article-title":"Co-evolution of proteins with their interaction partners.","volume":"299","year":"2000","journal-title":"J Mol Biol"},{"key":"pcbi-0010026-b07","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1093\/protein\/14.9.609","article-title":"Similarity of phylogenetic trees as indicator of protein\u2013protein interaction.","volume":"14","year":"2001","journal-title":"Protein Eng"},{"key":"pcbi-0010026-b08","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1002\/prot.340180402","article-title":"Correlated mutations and residue contacts in proteins.","volume":"18","year":"1994","journal-title":"Proteins"},{"key":"pcbi-0010026-b09","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1002\/prot.10074","article-title":"In silico two-hybrid system for the selection of physically interacting protein pairs.","volume":"47","year":"2002","journal-title":"Proteins"},{"key":"pcbi-0010026-b10","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1101\/gr.1145203","article-title":"Multimeric threading-based prediction of protein\u2013protein interactions on a genomic scale: Application to the Saccharomyces cerevisiae proteome.","volume":"13","year":"2003","journal-title":"Genome Res"},{"key":"pcbi-0010026-b11","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1002\/prot.10222","article-title":"MULTIPROSPECTOR: An algorithm for the prediction of protein\u2013protein interactions by multimeric threading.","volume":"49","year":"2002","journal-title":"Proteins"},{"key":"pcbi-0010026-b12","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1126\/science.1087361","article-title":"A Bayesian networks approach for predicting protein\u2013protein interactions from genomic data.","volume":"302","year":"2003","journal-title":"Science"},{"key":"pcbi-0010026-b13","doi-asserted-by":"crossref","first-page":"1107","DOI":"10.1101\/gr.1774904","article-title":"Annotation transfer between genomes: protein\u2013protein interologs and protein\u2013DNA regulogs.","volume":"14","year":"2004","journal-title":"Genome Res"},{"key":"pcbi-0010026-b14","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1126\/science.287.5450.116","article-title":"Protein interaction mapping in C. elegans using proteins involved in vulval development.","volume":"287","year":"2000","journal-title":"Science"},{"key":"pcbi-0010026-b15","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1146\/annurev.biophys.26.1.259","article-title":"Modular peptide recognition domains in eukaryotic signaling.","volume":"26","year":"1997","journal-title":"Annu Rev Biophys Biomol Struct"},{"key":"pcbi-0010026-b16","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.febslet.2004.03.116","article-title":"Selectivity and promiscuity in the interaction network mediated by protein recognition modules.","volume":"567","year":"2004","journal-title":"FEBS Lett"},{"key":"pcbi-0010026-b17","doi-asserted-by":"crossref","first-page":"4396","DOI":"10.1128\/MCB.6.12.4396","article-title":"A noncatalytic domain conserved among cytoplasmic protein-tyrosine kinases modifies the kinase function and transforming activity of Fujinami sarcoma virus P130gag-fps.","volume":"6","year":"1986","journal-title":"Mol Cell Biol"},{"key":"pcbi-0010026-b18","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/332272a0","article-title":"A novel viral oncogene with structural similarity to phospholipase C.","volume":"332","year":"1988","journal-title":"Nature"},{"key":"pcbi-0010026-b19","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1126\/science.1379745","article-title":"Identification of a protein that binds to the SH3 region of Abl and is similar to Bcr and GAP-rho.","volume":"257","year":"1992","journal-title":"Science"},{"key":"pcbi-0010026-b20","doi-asserted-by":"crossref","first-page":"1157","DOI":"10.1126\/science.8438166","article-title":"Identification of a ten-amino acid proline-rich SH3 binding site.","volume":"259","year":"1993","journal-title":"Science"},{"key":"pcbi-0010026-b21","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1006\/jmbi.2000.3670","article-title":"SH3-SPOT: An algorithm to predict preferred ligands to different members of the SH3 gene family.","volume":"298","year":"2000","journal-title":"J Mol Biol"},{"key":"pcbi-0010026-b22","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1126\/science.1064987","article-title":"A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.","volume":"295","year":"2002","journal-title":"Science"},{"key":"pcbi-0010026-b23","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nrm1589","article-title":"Intrinsically unstructured proteins and their functions.","volume":"6","year":"2005","journal-title":"Nat Rev Mol Cell Biol"},{"key":"pcbi-0010026-b24","doi-asserted-by":"crossref","first-page":"6573","DOI":"10.1021\/bi012159+","article-title":"Intrinsic disorder and protein function.","volume":"41","year":"2002","journal-title":"Biochemistry"},{"key":"pcbi-0010026-b25","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/S0968-0004(02)02169-2","article-title":"Intrinsically unstructured proteins.","volume":"27","year":"2002","journal-title":"Trends Biochem Sci"},{"key":"pcbi-0010026-b26","doi-asserted-by":"crossref","first-page":"1046","DOI":"10.1038\/sj.embor.7400276","article-title":"Natively unfolded domains in endocytosis: Hooks, lines and linkers.","volume":"5","year":"2004","journal-title":"EMBO Rep"},{"key":"pcbi-0010026-b27","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1016\/S0092-8674(00)80463-8","article-title":"Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: A model for activator:coactivator interactions.","volume":"91","year":"1997","journal-title":"Cell"},{"key":"pcbi-0010026-b28","doi-asserted-by":"crossref","first-page":"18638","DOI":"10.1074\/jbc.M300518200","article-title":"The C-terminal domain of the measles virus nucleoprotein is intrinsically disordered and folds upon binding to the C-terminal moiety of the phosphoprotein.","volume":"278","year":"2003","journal-title":"J Biol Chem"},{"key":"pcbi-0010026-b29","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1016\/S0959-440X(02)00289-0","article-title":"Coupling of folding and binding for unstructured proteins.","volume":"12","year":"2002","journal-title":"Curr Opin Struct Biol"},{"key":"pcbi-0010026-b30","doi-asserted-by":"crossref","first-page":"3701","DOI":"10.1093\/nar\/gkg519","article-title":"GlobPlot: Exploring protein sequences for globularity and disorder.","volume":"31","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0010026-b31","doi-asserted-by":"crossref","unstructured":"MayerBJSakselaK\n\t\t\t\t\t2005\n\t\t\t\t\tSH3 domains.\n\t\t\t\t\tIn:\n\t\t\t\t\tCesarenniGGimonaMSudolMYaffeM\n\t\t\t\t\tModular protein domains\n\t\t\t\t\tWeinheim (Germany)\n\t\t\t\t\tWiley-VCH\n\t\t\t\t\tpp.\n\t\t\t\t\t46\n\t\t\t\t\t55","DOI":"10.1002\/3527603611.ch2"},{"key":"pcbi-0010026-b32","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1038\/nature02579","article-title":"Genome evolution in yeasts.","volume":"430","year":"2004","journal-title":"Nature"},{"key":"pcbi-0010026-b33","doi-asserted-by":"crossref","first-page":"7329","DOI":"10.1073\/pnas.0401648101","article-title":"The diploid genome sequence of Candida albicans.","volume":"101","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pcbi-0010026-b34","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1038\/nature01644","article-title":"Sequencing and comparison of yeast species to identify genes and regulatory elements.","volume":"423","year":"2003","journal-title":"Nature"},{"key":"pcbi-0010026-b35","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1126\/science.1084337","article-title":"Finding functional features in Saccharomyces genomes by phylogenetic footprinting.","volume":"301","year":"2003","journal-title":"Science"},{"key":"pcbi-0010026-b36","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1038\/nature01554","article-title":"The genome sequence of the filamentous fungus Neurospora crassa.","volume":"422","year":"2003","journal-title":"Nature"},{"key":"pcbi-0010026-b37","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1038\/nature724","article-title":"The genome sequence of Schizosaccharomyces pombe.","volume":"415","year":"2002","journal-title":"Nature"},{"key":"pcbi-0010026-b38","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: A novel method for fast and accurate multiple sequence alignment.","volume":"302","year":"2000","journal-title":"J Mol Biol"},{"key":"pcbi-0010026-b39","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1126\/science.278.5338.631","article-title":"A genomic perspective on protein families.","volume":"278","year":"1997","journal-title":"Science"},{"key":"pcbi-0010026-b40","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1002\/(SICI)1097-0134(199703)27:3<329::AID-PROT1>3.0.CO;2-8","article-title":"Seventy-five percent accuracy in protein secondary structure prediction.","volume":"27","year":"1997","journal-title":"Proteins"},{"key":"pcbi-0010026-b41","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1146\/annurev.biochem.73.011303.073950","article-title":"Analyzing cellular biochemistry in terms of molecular networks.","volume":"73","year":"2004","journal-title":"Annu Rev Biochem"},{"key":"pcbi-0010026-b42","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1002\/(SICI)1097-0061(19980330)14:5<443::AID-YEA243>3.0.CO;2-L","article-title":"Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi.","volume":"14","year":"1998","journal-title":"Yeast"},{"key":"pcbi-0010026-b43","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1038\/nrg929","article-title":"The origin and evolution of model organisms.","volume":"3","year":"2002","journal-title":"Nat Rev Genet"},{"key":"pcbi-0010026-b44","article-title":"A model of the statistical power of comparative genome sequence analysis.","volume":"3","year":"2005","journal-title":"PLoS Biol"},{"key":"pcbi-0010026-b45","article-title":"Conservation and evolution of cis-regulatory systems in ascomycete fungi.","volume":"2","year":"2004","journal-title":"PLoS Biol"},{"key":"pcbi-0010026-b46","doi-asserted-by":"crossref","first-page":"3710","DOI":"10.1093\/bioinformatics\/bth456","article-title":"GO::TermFinder\u2014Open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.","volume":"20","year":"2004","journal-title":"Bioinformatics"},{"key":"pcbi-0010026-b47","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.1091\/mbc.e02-08-0501","article-title":"Drs2p-related P-type ATPases Dnf1p and Dnf2p are required for phospholipid translocation across the yeast plasma membrane and serve a role in endocytosis.","volume":"14","year":"2003","journal-title":"Mol Biol Cell"},{"key":"pcbi-0010026-b48","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1016\/S0955-0674(01)00297-6","article-title":"Coupling actin dynamics and membrane dynamics during endocytosis.","volume":"14","year":"2002","journal-title":"Curr Opin Cell Biol"},{"key":"pcbi-0010026-b49","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1083\/jcb.200305007","article-title":"Vps27\u2013Hse1 and ESCRT-I complexes cooperate to increase efficiency of sorting ubiquitinated proteins at the endosome.","volume":"163","year":"2003","journal-title":"J Cell Biol"},{"key":"pcbi-0010026-b50","doi-asserted-by":"crossref","first-page":"534","DOI":"10.1038\/ncb815","article-title":"The Vps27p Hse1p complex binds ubiquitin and mediates endosomal protein sorting.","volume":"4","year":"2002","journal-title":"Nat Cell Biol"},{"key":"pcbi-0010026-b51","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1016\/S1369-5274(00)00143-0","article-title":"Pheromone response, mating and cell biology.","volume":"3","year":"2000","journal-title":"Curr Opin Microbiol"},{"key":"pcbi-0010026-b52","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1002\/j.1460-2075.1996.tb00336.x","article-title":"The SLT2(MPK1) MAP kinase is activated during periods of polarized cell growth in yeast.","volume":"15","year":"1996","journal-title":"EMBO J"},{"key":"pcbi-0010026-b53","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1016\/S0962-8924(98)01491-3","article-title":"Gettin' down with ubiquitin: Turning off cell-surface receptors, transporters and channels.","volume":"9","year":"1999","journal-title":"Trends Cell Biol"},{"key":"pcbi-0010026-b54","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.1016\/S0022-2836(03)00664-8","article-title":"Ligand screening by exoproteolysis and mass spectrometry in combination with computer modelling.","volume":"330","year":"2003","journal-title":"J Mol Biol"},{"key":"pcbi-0010026-b55","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1016\/j.jmb.2005.02.046","article-title":"Recognizing and defining true Ras binding domains II: In silico prediction based on homology modelling and energy calculations.","volume":"348","year":"2005","journal-title":"J Mol Biol"},{"key":"pcbi-0010026-b56","doi-asserted-by":"crossref","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","article-title":"CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.","volume":"22","year":"1994","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0010026-b57","doi-asserted-by":"crossref","first-page":"D142","DOI":"10.1093\/nar\/gkh088","article-title":"SMART 4.0: Towards genomic data integration.","volume":"32","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0010026-b58","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/nar\/28.1.37","article-title":"MIPS: A database for genomes and protein sequences.","volume":"28","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0010026-b59","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1093\/nar\/28.1.289","article-title":"DIP: The database of interacting proteins.","volume":"28","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pcbi-0010026-b60","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1016\/S0014-5793(01)03293-8","article-title":"MINT: A Molecular INTeraction database.","volume":"513","year":"2002","journal-title":"FEBS Lett"},{"key":"pcbi-0010026-b61","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1093\/nar\/29.1.242","article-title":"BIND\u2014The Biomolecular Interaction Network Database.","volume":"29","year":"2001","journal-title":"Nucleic Acids Res"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0010026","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,6]],"date-time":"2020-05-06T21:28:21Z","timestamp":1588800501000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.0010026"}},"subtitle":[],"editor":[{"given":"Mark","family":"Gerstein","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2005,8,12]]},"references-count":61,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2005,8,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.0010026","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2005,8,12]]}}}