{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2022,12,17]],"date-time":"2022-12-17T00:57:24Z","timestamp":1671238644347},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"S2","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>The protein-protein interaction (PPI) is one of the most important features to understand biological processes. For a PPI, the physical domain-domain interaction (DDI) plays the key role for biology functions. In the post-genomic era, to rapidly identify homologous PPIs for analyzing the contact residue pairs of their interfaces within DDIs on a genomic scale is essential to determine PPI networks and the PPI interface evolution across multiple species.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this study, we proposed \"pair <jats:underline>P<\/jats:underline> osition <jats:underline>S<\/jats:underline> pecific <jats:underline>S<\/jats:underline> coring <jats:underline>M<\/jats:underline> atrix (<jats:italic>pair<\/jats:italic> PSSM)\" to identify homologous PPIs. The <jats:italic>pair<\/jats:italic> PSSM can successfully distinguish the true protein complexes from unreasonable protein pairs with about 90% accuracy. For the test set including 1,122 representative heterodimers and 2,708,746 non-interacting protein pairs, the mean average precision and mean false positive rate of <jats:italic>pair<\/jats:italic> PSSM were 0.42 and 0.31, respectively. Moreover, we applied <jats:italic>pair<\/jats:italic> PSSM to identify ~450,000 homologous PPIs with their interacting domains and residues in seven common organisms (e.g. <jats:italic>Homo sapiens<\/jats:italic>, <jats:italic>Mus musculus<\/jats:italic>, <jats:italic>Saccharomyces cerevisiae<\/jats:italic> and <jats:italic>Escherichia coli<\/jats:italic>).<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Our <jats:italic>pair<\/jats:italic> PSSM is able to provide statistical significance of residue pairs using evolutionary profiles and a scoring system for inferring homologous PPIs. According to our best knowledge, the <jats:italic>pair<\/jats:italic> PSSM is the first method for searching homologous PPIs across multiple species using pair position specific scoring matrix and a 3D dimer as the template to map interacting domain pairs of these PPIs. We believe that <jats:italic>pair<\/jats:italic> PSSM is able to provide valuable insights for the PPI evolution and networks across multiple species.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-14-s2-s11","type":"journal-article","created":{"date-parts":[[2013,1,21]],"date-time":"2013-01-21T15:16:08Z","timestamp":1358781368000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Inferring homologous protein-protein interactions through pair position specific scoring matrix"],"prefix":"10.1186","volume":"14","author":[{"given":"Chun-Yu","family":"Lin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yung-Chiang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yu-Shu","family":"Lo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jinn-Moon","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2013,1,21]]},"reference":[{"key":"5600_CR1","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1038\/nature750","volume":"417","author":"C von Mering","year":"2002","unstructured":"von Mering C, Krause R, Snel B, Cornell M, Oliver SG, Fields S, Bork P: Comparative assessment of large-scale data sets of protein-protein interactions. 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