{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,13]],"date-time":"2024-09-13T21:36:46Z","timestamp":1726263406646},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2023,3,1]],"date-time":"2023-03-01T00:00:00Z","timestamp":1677628800000},"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\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61772217","62172172"],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Scientific Research Start-up Foundation of Binzhou Medical University","award":["BY2020KYQD01"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,3,19]]},"abstract":"Abstract<\/jats:title>Neuropeptides are a diverse and complex class of signaling molecules that regulate a variety of biological processes. Neuropeptides provide many opportunities for the discovery of new drugs and targets for the treatment of a wide range of diseases, and thus, computational tools for the rapid and accurate large-scale identification of neuropeptides are of great significance for peptide research and drug development. Although several machine learning-based prediction tools have been developed, there is room for improvement in the performance and interpretability of the proposed methods. In this work, we developed an interpretable and robust neuropeptide prediction model, named NeuroPred-PLM. First, we employed a language model (ESM) of proteins to obtain semantic representations of neuropeptides, which could reduce the complexity of feature engineering. Next, we adopted a multi-scale convolutional neural network to enhance the local feature representation of neuropeptide embeddings. To make the model interpretable, we proposed a global multi-head attention network that could be used to capture the position-wise contribution to neuropeptide prediction via the attention scores. In addition, NeuroPred-PLM was developed based on our newly constructed NeuroPep 2.0 database. Benchmarks based on the independent test set show that NeuroPred-PLM achieves superior predictive performance compared with other state-of-the-art predictors. For the convenience of researchers, we provide an easy-to-install PyPi package (https:\/\/pypi.org\/project\/NeuroPredPLM\/) and a web server (https:\/\/huggingface.co\/spaces\/isyslab\/NeuroPred-PLM).<\/jats:p>","DOI":"10.1093\/bib\/bbad077","type":"journal-article","created":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T15:14:26Z","timestamp":1676474066000},"source":"Crossref","is-referenced-by-count":17,"title":["NeuroPred-PLM: an interpretable and robust model for neuropeptide prediction by protein language model"],"prefix":"10.1093","volume":"24","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-0168-9730","authenticated-orcid":false,"given":"Lei","family":"Wang","sequence":"first","affiliation":[{"name":"Institute of Medical Artificial Intelligence, Binzhou Medical University , Yantai, Shandong 264003 , China"},{"name":"School of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei 430074 , China"}]},{"given":"Chen","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Software Engineering, Huazhong University of Science and Technology , Wuhan, Hubei 430074 , China"}]},{"given":"Mingxia","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Medical Artificial Intelligence, Binzhou Medical University , Yantai, Shandong 264003 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0003-3559-0867","authenticated-orcid":false,"given":"Zhidong","family":"Xue","sequence":"additional","affiliation":[{"name":"Institute of Medical Artificial Intelligence, Binzhou Medical University , Yantai, Shandong 264003 , China"},{"name":"School of Software Engineering, Huazhong University of Science and Technology , Wuhan, Hubei 430074 , China"}]},{"ORCID":"http:\/\/orcid.org\/0000-0002-2823-5886","authenticated-orcid":false,"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Medical Artificial Intelligence, Binzhou Medical University , Yantai, Shandong 264003 , China"},{"name":"School of Life Science and Technology, Huazhong University of Science and Technology , Wuhan, Hubei 430074 , China"}]}],"member":"286","published-online":{"date-parts":[[2023,3,9]]},"reference":[{"key":"2023032006153314600_","doi-asserted-by":"crossref","first-page":"114129","DOI":"10.1016\/j.bcp.2020.114129","article-title":"Neuropeptide signalling systems - an underexplored target for venom drug discovery","volume":"181","author":"Mendel","year":"2020","journal-title":"Biochem Pharmacol"},{"key":"2023032006153314600_","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/978-1-61779-310-3_1","article-title":"What are neuropeptides?","volume":"789","author":"Burbach","year":"2011","journal-title":"Methods Mol Biol"},{"key":"2023032006153314600_","doi-asserted-by":"crossref","first-page":"bav038","DOI":"10.1093\/database\/bav038","article-title":"NeuroPep: a comprehensive resource of 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