{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T22:17:56Z","timestamp":1780438676136,"version":"3.54.1"},"reference-count":235,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,5,13]],"date-time":"2024-05-13T00:00:00Z","timestamp":1715558400000},"content-version":"vor","delay-in-days":47,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62225209"],"award-info":[{"award-number":["62225209"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science and Technology Innovation Program of Hunan Province","award":["2021RC0048"],"award-info":[{"award-number":["2021RC0048"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Proteins interact with diverse ligands to perform a large number of biological functions, such as gene expression and signal transduction. Accurate identification of these protein\u2013ligand interactions is crucial to the understanding of molecular mechanisms and the development of new drugs. However, traditional biological experiments are time-consuming and expensive. With the development of high-throughput technologies, an increasing amount of protein data is available. In the past decades, many computational methods have been developed to predict protein\u2013ligand interactions. Here, we review a comprehensive set of over 160 protein\u2013ligand interaction predictors, which cover protein\u2013protein, protein\u2212nucleic acid, protein\u2212peptide and protein\u2212other ligands (nucleotide, heme, ion) interactions. We have carried out a comprehensive analysis of the above four types of predictors from several significant perspectives, including their inputs, feature profiles, models, availability, etc. The current methods primarily rely on protein sequences, especially utilizing evolutionary information. The significant improvement in predictions is attributed to deep learning methods. Additionally, sequence-based pretrained models and structure-based approaches are emerging as new trends.<\/jats:p>","DOI":"10.1093\/bib\/bbae162","type":"journal-article","created":{"date-parts":[[2024,5,13]],"date-time":"2024-05-13T09:24:14Z","timestamp":1715592254000},"source":"Crossref","is-referenced-by-count":10,"title":["A comprehensive review of protein-centric predictors for biomolecular interactions: from proteins to nucleic acids and beyond"],"prefix":"10.1093","volume":"25","author":[{"given":"Pengzhen","family":"Jia","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , 932 Lushan Road(S), Changsha 410083 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fuhao","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , 932 Lushan Road(S), Changsha 410083 , China"},{"name":"College of Information Engineering, Northwest A&F University , No. 3 Taicheng Road, Yangling, Shaanxi 712100 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaojin","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , 932 Lushan Road(S), Changsha 410083 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0188-1394","authenticated-orcid":false,"given":"Min","family":"Li","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , 932 Lushan Road(S), Changsha 410083 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,5,12]]},"reference":[{"issue":"1","key":"2024051309031376900_ref1","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1093\/bioinformatics\/btab643","article-title":"Structure-aware protein\u2013protein interaction site 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