{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:28Z","timestamp":1772138068446,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,5,6]],"date-time":"2024-05-06T00:00:00Z","timestamp":1714953600000},"content-version":"vor","delay-in-days":5,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Integrative Immuno-Oncology","award":["351507"],"award-info":[{"award-number":["351507"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Peptide therapeutics hinge on the precise interaction between a tailored peptide and its designated receptor while mitigating interactions with alternate receptors is equally indispensable. Existing methods primarily estimate the binding score between protein and peptide pairs. However, for a specific peptide without a corresponding protein, it is challenging to identify the proteins it could bind due to the sheer number of potential candidates.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a transformers-based protein embedding scheme in this study that can quickly identify and rank millions of interacting proteins. Furthermore, the proposed approach outperforms existing sequence- and structure-based methods, with a mean AUC-ROC and AUC-PR of 0.73.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Training data, scripts, and fine-tuned parameters are available at https:\/\/github.com\/RoniGurvich\/Peptriever. The proposed method is linked with a web application available for customized prediction at https:\/\/peptriever.app\/.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae303","type":"journal-article","created":{"date-parts":[[2024,5,6]],"date-time":"2024-05-06T19:22:45Z","timestamp":1715023365000},"source":"Crossref","is-referenced-by-count":2,"title":["Peptriever: a Bi-Encoder approach for large-scale protein\u2013peptide binding search"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-9942-6775","authenticated-orcid":false,"given":"Roni","family":"Gurvich","sequence":"first","affiliation":[{"name":"Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital , Petah Tikva 49100, Israel"}]},{"given":"Gal","family":"Markel","sequence":"additional","affiliation":[{"name":"Davidoff Cancer Center, Rabin Medical Center-Beilinson Hospital , Petah Tikva 49100, Israel"},{"name":"Faculty of Medicine, Tel Aviv University , 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