Shaojun Wang , Ronghui You , Yunjia Liu , Yi Xiong , Shanfeng Zhu
{"title":"NetGO 3.0:蛋白质语言模型改进了大规模功能注释。","authors":"Shaojun Wang , Ronghui You , Yunjia Liu , Yi Xiong , Shanfeng Zhu","doi":"10.1016/j.gpb.2023.04.001","DOIUrl":null,"url":null,"abstract":"<div><p>As one of the state-of-the-art automated function prediction (AFP) methods, NetGO 2.0 integrates multi-source information to improve the performance. However, it mainly utilizes the proteins with experimentally supported functional annotations without leveraging valuable information from a vast number of unannotated proteins. Recently, <strong>protein language models</strong> have been proposed to learn informative representations [<em>e.g.</em>, Evolutionary Scale Modeling (ESM)-1b embedding] from protein sequences based on self-supervision. Here, we represented each protein by ESM-1b and used logistic regression (LR) to train a new model, LR-ESM, for AFP. The experimental results showed that LR-ESM achieved comparable performance with the best-performing component of NetGO 2.0. Therefore, by incorporating LR-ESM into NetGO 2.0, we developed NetGO 3.0 to improve the performance of AFP extensively. NetGO 3.0 is freely accessible at <span>https://dmiip.sjtu.edu.cn/ng3.0</span><svg><path></path></svg>.</p></div>","PeriodicalId":12528,"journal":{"name":"Genomics, Proteomics & Bioinformatics","volume":"21 2","pages":"Pages 349-358"},"PeriodicalIF":11.5000,"publicationDate":"2023-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"6","resultStr":"{\"title\":\"NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations\",\"authors\":\"Shaojun Wang , Ronghui You , Yunjia Liu , Yi Xiong , Shanfeng Zhu\",\"doi\":\"10.1016/j.gpb.2023.04.001\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>As one of the state-of-the-art automated function prediction (AFP) methods, NetGO 2.0 integrates multi-source information to improve the performance. However, it mainly utilizes the proteins with experimentally supported functional annotations without leveraging valuable information from a vast number of unannotated proteins. Recently, <strong>protein language models</strong> have been proposed to learn informative representations [<em>e.g.</em>, Evolutionary Scale Modeling (ESM)-1b embedding] from protein sequences based on self-supervision. Here, we represented each protein by ESM-1b and used logistic regression (LR) to train a new model, LR-ESM, for AFP. The experimental results showed that LR-ESM achieved comparable performance with the best-performing component of NetGO 2.0. Therefore, by incorporating LR-ESM into NetGO 2.0, we developed NetGO 3.0 to improve the performance of AFP extensively. NetGO 3.0 is freely accessible at <span>https://dmiip.sjtu.edu.cn/ng3.0</span><svg><path></path></svg>.</p></div>\",\"PeriodicalId\":12528,\"journal\":{\"name\":\"Genomics, Proteomics & Bioinformatics\",\"volume\":\"21 2\",\"pages\":\"Pages 349-358\"},\"PeriodicalIF\":11.5000,\"publicationDate\":\"2023-04-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"6\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Genomics, Proteomics & Bioinformatics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1672022923000669\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Genomics, Proteomics & Bioinformatics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1672022923000669","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
NetGO 3.0: Protein Language Model Improves Large-scale Functional Annotations
As one of the state-of-the-art automated function prediction (AFP) methods, NetGO 2.0 integrates multi-source information to improve the performance. However, it mainly utilizes the proteins with experimentally supported functional annotations without leveraging valuable information from a vast number of unannotated proteins. Recently, protein language models have been proposed to learn informative representations [e.g., Evolutionary Scale Modeling (ESM)-1b embedding] from protein sequences based on self-supervision. Here, we represented each protein by ESM-1b and used logistic regression (LR) to train a new model, LR-ESM, for AFP. The experimental results showed that LR-ESM achieved comparable performance with the best-performing component of NetGO 2.0. Therefore, by incorporating LR-ESM into NetGO 2.0, we developed NetGO 3.0 to improve the performance of AFP extensively. NetGO 3.0 is freely accessible at https://dmiip.sjtu.edu.cn/ng3.0.
期刊介绍:
Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.