{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T06:57:54Z","timestamp":1771916274062,"version":"3.50.1"},"reference-count":48,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2023,10,24]],"date-time":"2023-10-24T00:00:00Z","timestamp":1698105600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42171450"],"award-info":[{"award-number":["42171450"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Quantitative determination of protein thermodynamic stability is a critical step in protein and drug design. Reliable prediction of protein stability changes caused by point variations contributes to developing-related fields. Over the past decades, dozens of structure-based and sequence-based methods have been proposed, showing good prediction performance. Despite the impressive progress, it is necessary to explore wild-type and variant protein representations to address the problem of how to represent the protein stability change in view of global sequence. With the development of structure prediction using learning-based methods, protein language models (PLMs) have shown accurate and high-quality predictions of protein structure. Because PLM captures the atomic-level structural information, it can help to understand how single-point variations cause functional changes.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we proposed THPLM, a sequence-based deep learning model for stability change prediction using Meta\u2019s ESM-2. With ESM-2 and a simple convolutional neural network, THPLM achieved comparable or even better performance than most methods, including sequence-based and structure-based methods. Furthermore, the experimental results indicate that the PLM\u2019s ability to generate representations of sequence can effectively improve the ability of protein function prediction.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code of THPLM and the testing data can be accessible through the following links: https:\/\/github.com\/FPPGroup\/THPLM.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad646","type":"journal-article","created":{"date-parts":[[2023,10,24]],"date-time":"2023-10-24T19:52:18Z","timestamp":1698177138000},"source":"Crossref","is-referenced-by-count":30,"title":["THPLM: a sequence-based deep learning framework for protein stability changes prediction upon point variations using pretrained protein language model"],"prefix":"10.1093","volume":"39","author":[{"given":"Jianting","family":"Gong","sequence":"first","affiliation":[{"name":"School of Information Science and Technology, Institution of Computational Biology, Northeast Normal University , Changchun 130117, China"},{"name":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Changchun 130122, China"}]},{"given":"Lili","family":"Jiang","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, Institution of Computational Biology, Northeast Normal University , Changchun 130117, China"},{"name":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences , Changchun 130122, China"}]},{"given":"Yongbing","family":"Chen","sequence":"additional","affiliation":[{"name":"School of Information Science and Technology, Institution of Computational Biology, Northeast Normal University , Changchun 130117, China"},{"name":"Changchun Veterinary Research 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