{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T18:06:29Z","timestamp":1775325989493,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2020,8,6]],"date-time":"2020-08-06T00:00:00Z","timestamp":1596672000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100002809","name":"Government of Catalonia","doi-asserted-by":"publisher","award":["2018FI_B_00873"],"award-info":[{"award-number":["2018FI_B_00873"]}],"id":[{"id":"10.13039\/501100002809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Spanish government","award":["BIO2016-79930-R"],"award-info":[{"award-number":["BIO2016-79930-R"]}]},{"name":"Spanish government","award":["PID2019-110167RB-I00"],"award-info":[{"award-number":["PID2019-110167RB-I00"]}]},{"name":"Spanish government","award":["CTQ2016-79138-R"],"award-info":[{"award-number":["CTQ2016-79138-R"]}]},{"name":"EU European Regional Development Fund program Interreg V-A Spain-France-Andorra"},{"name":"IBM-BSC Deep Learning Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single protein residue mutations may reshape the binding affinity of protein\u2013protein interactions. Therefore, predicting its effects is of great interest in biotechnology and biomedicine. Unfortunately, the availability of experimental data on binding affinity changes upon mutation is limited, which hampers the development of new and more precise algorithms. Here, we propose UEP, a classifier for predicting beneficial and detrimental mutations in protein\u2013protein complexes trained on interactome data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Regardless of the simplicity of the UEP algorithm, which is based on a simple three-body contact potential derived from interactome data, we report competitive results with the gold standard methods in this field with the advantage of being faster in terms of computational time. Moreover, we propose a consensus selection procedure by involving the combination of three predictors that showed higher classification accuracy in our benchmark: UEP, pyDock and EvoEF1\/FoldX. Overall, we demonstrate that the analysis of interactome data allows predicting the impact of protein\u2013protein mutations using UEP, a fast and reliable open-source code.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>UEP algorithm can be found at: https:\/\/github.com\/pepamengual\/UEP.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa708","type":"journal-article","created":{"date-parts":[[2020,7,31]],"date-time":"2020-07-31T11:29:59Z","timestamp":1596194999000},"page":"334-341","source":"Crossref","is-referenced-by-count":7,"title":["UEP: an open-source and fast classifier for predicting the impact of mutations in protein\u2013protein complexes"],"prefix":"10.1093","volume":"37","author":[{"given":"Pep","family":"Amengual-Rigo","sequence":"first","affiliation":[{"name":"Department of Life Sciences, Barcelona Supercomputing Center (BSC) , 08034 Barcelona, Spain"}]},{"given":"Juan","family":"Fern\u00e1ndez-Recio","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Barcelona Supercomputing Center (BSC) , 08034 Barcelona, Spain"},{"name":"Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de la Rioja-Gobierno de la Rioja , 26007 Logro\u00f1o, Spain"}]},{"given":"Victor","family":"Guallar","sequence":"additional","affiliation":[{"name":"Department of Life Sciences, Barcelona Supercomputing Center (BSC) , 08034 Barcelona, Spain"},{"name":"ICREA: Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats , 08010 Barcelona, Spain"}]}],"member":"286","published-online":{"date-parts":[[2020,8,6]]},"reference":[{"key":"2023051604083927300_btaa708-B1","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\u2013protein docking","volume":"68","author":"Cheng","year":"2007","journal-title":"Proteins Struct. 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