{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T18:07:40Z","timestamp":1793383660422,"version":"4.5.0"},"reference-count":56,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,10,20]],"date-time":"2021-10-20T00:00:00Z","timestamp":1634688000000},"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\/100009174","name":"National Agricultural Statistics Service","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009174","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001503","name":"Indian Council of Agricultural Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001503","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Fungal infections or mycosis cause a wide range of diseases in humans and animals. The incidences of community acquired; nosocomial fungal infections have increased dramatically after the emergence of COVID-19 pandemic. The increase in number of patients with immunodeficiency \/ immunosuppression related diseases, resistance to existing antifungal compounds and availability of limited therapeutic options has triggered the search for alternative antifungal molecules. In this direction, antifungal peptides (AFPs) have received a lot of interest as an alternative to currently available antifungal drugs. Although the AFPs are produced by diverse population of living organisms, identifying effective AFPs from natural sources is time-consuming and expensive. Therefore, there is a need to develop a robust in silico model capable of identifying novel AFPs in protein sequences. In this paper, we propose Deep-AFPpred, a deep learning classifier that can identify AFPs in protein sequences. We developed Deep-AFPpred using the concept of transfer learning with 1DCNN-BiLSTM deep learning algorithm. The findings reveal that Deep-AFPpred beats other state-of-the-art AFP classifiers by a wide margin and achieved approximately 96% and 94% precision on validation and test data, respectively. Based on the proposed approach, an online prediction server is created and made publicly available at https:\/\/afppred.anvil.app\/. Using this server, one can identify novel AFPs in protein sequences and the results are provided as a report that includes predicted peptides, their physicochemical properties and motifs. By utilizing this model, we identified AFPs in different proteins, which can be chemically synthesized in lab and experimentally validated for their antifungal activity.<\/jats:p>","DOI":"10.1093\/bib\/bbab422","type":"journal-article","created":{"date-parts":[[2021,9,19]],"date-time":"2021-09-19T11:07:04Z","timestamp":1632049624000},"source":"Crossref","is-referenced-by-count":66,"title":["Deep-AFPpred: identifying novel antifungal peptides using pretrained embeddings from seq2vec with 1DCNN-BiLSTM"],"prefix":"10.1093","volume":"23","author":[{"given":"Ritesh","family":"Sharma","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering , Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sameer","family":"Shrivastava","sequence":"additional","affiliation":[{"name":"Division of Veterinary Biotechnology , ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjay","family":"Kumar Singh","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering , Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abhinav","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering , Indian Institute of Technology (BHU), Varanasi, 221005, Uttar Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sonal","family":"Saxena","sequence":"additional","affiliation":[{"name":"Division of Veterinary Biotechnology , ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raj","family":"Kumar Singh","sequence":"additional","affiliation":[{"name":"Former Director & Vice Chancellor , ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,10,20]]},"reference":[{"key":"2022102000070410300_ref1","doi-asserted-by":"crossref","first-page":"117s","DOI":"10.1111\/j.1365-2672.1989.tb03776.x","article-title":"Fungi in the production of foods and food ingredients","volume":"67","author":"Campbell-Platt","year":"1989","journal-title":"J Appl Bacteriol"},{"key":"2022102000070410300_ref2","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1016\/B978-0-12-382034-1.00012-8","volume-title":"The Fungi","author":"Money","year":"2016"},{"key":"2022102000070410300_ref3","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1007\/978-981-13-0393-7_6","volume-title":"Fungi and Their Role in Sustainable Development: Current Perspectives","author":"Mukherjee","year":"2018"},{"key":"2022102000070410300_ref4","doi-asserted-by":"crossref","first-page":"105","DOI":"10.3389\/fcimb.2020.00105","article-title":"Antifungal peptides as therapeutic agents","volume":"10","author":"Fern\u00e1ndez de Ullivarri","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"issue":"5","key":"2022102000070410300_ref5","doi-asserted-by":"crossref","first-page":"a019703","DOI":"10.1101\/cshperspect.a019703","article-title":"Antifungal drug development: challenges, unmet clinical needs, and new approaches","volume":"4","author":"Roemer","year":"2014","journal-title":"Cold Spring Harb Perspect Med"},{"key":"2022102000070410300_ref6","doi-asserted-by":"crossref","first-page":"57","DOI":"10.3390\/jof3040057","article-title":"HIV\u2013associated cryptococcal disease in resource-limited setting: a case for prevention is better than cure. 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