{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,24]],"date-time":"2025-03-24T08:51:12Z","timestamp":1742806272656,"version":"3.37.3"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,7]],"date-time":"2022-05-07T00:00:00Z","timestamp":1651881600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["051\/2013"],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004901","name":"Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004901","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100012116","name":"European Bioinformatics Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100012116","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AA123456","BB123456"],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Alcohol & Education Research Council","award":["abcde123456"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"Abstract<\/jats:title>\n Proteins are essential macromolecules for the maintenance of living systems. Many of them perform their function by interacting with other molecules in regions called binding sites. The identification and characterization of these regions are of fundamental importance to determine protein function, being a fundamental step in processes such as drug design and discovery. However, identifying such binding regions is not trivial due to the drawbacks of experimental methods, which are costly and time-consuming. Here we propose GRaSP-web, a web server that uses GRaSP (Graph-based Residue neighborhood Strategy to Predict binding sites), a residue-centric method based on graphs that uses machine learning to predict putative ligand binding site residues. The method outperformed 6 state-of-the-art residue-centric methods (MCC of 0.61). Also, GRaSP-web is scalable as it takes 10-20 seconds to predict binding sites for a protein complex (the state-of-the-art residue-centric method takes 2-5h on the average). It proved to be consistent in predicting binding sites for bound\/unbound structures (MCC 0.61 for both) and for a large dataset of multi-chain proteins (4500 entries, MCC 0.61). GRaSPWeb is freely available at https:\/\/grasp.ufv.br.<\/jats:p>","DOI":"10.1093\/nar\/gkac323","type":"journal-article","created":{"date-parts":[[2022,4,22]],"date-time":"2022-04-22T19:10:43Z","timestamp":1650654643000},"page":"W392-W397","source":"Crossref","is-referenced-by-count":12,"title":["GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs"],"prefix":"10.1093","volume":"50","author":[{"given":"Charles A","family":"Santana","sequence":"first","affiliation":[{"name":"Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais , Belo Horizonte\u00a031270-901, Brazil"},{"name":"Department of Computer Science, Universidade Federal de Minas Gerais , Belo Horizonte\u00a031270-901, Brazil"}]},{"given":"Sandro C","family":"Izidoro","sequence":"additional","affiliation":[{"name":"Institute of Technological Sciences (ICT), Advanced Campus at Itabira, Universidade Federal de Itajub\u00e1 , Itabira\u00a035903-087, Brazil"}]},{"given":"Raquel C","family":"de\u00a0Melo-Minardi","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais , Belo Horizonte\u00a031270-901, Brazil"},{"name":"Department of Computer Science, Universidade Federal de Minas Gerais , Belo Horizonte\u00a031270-901, Brazil"}]},{"given":"Jonathan\u00a0D","family":"Tyzack","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2533-1231","authenticated-orcid":false,"given":"Ant\u00f3nio J M","family":"Ribeiro","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3004-2119","authenticated-orcid":false,"given":"Douglas E V","family":"Pires","sequence":"additional","affiliation":[{"name":"School of Computing and Information Systems, University of Melbourne , Parkville\u00a03052, Australia"}]},{"given":"Janet\u00a0M","family":"Thornton","sequence":"additional","affiliation":[{"name":"European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus , Hinxton, Cambridge CB10 1SD, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4723-2349","authenticated-orcid":false,"given":"Sabrina","family":"de\u00a0A.\u00a0Silveira","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Universidade Federal de Vi\u00e7osa , Vi\u00e7osa\u00a036570-900, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2022,5,7]]},"reference":[{"key":"2022070423580055600_B1","doi-asserted-by":"crossref","first-page":"D412","DOI":"10.1093\/nar\/gkaa913","article-title":"Pfam: The protein families database in 2021","volume":"49","author":"Mistry","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2022070423580055600_B2","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.csbj.2020.02.008","article-title":"Exploring the computational methods for protein-ligand binding site prediction","volume":"18","author":"Zhao","year":"2020","journal-title":"Comput. 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Cheminformatics"},{"key":"2022070423580055600_B29","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkz424","article-title":"PrankWeb: a web server for ligand binding site prediction and visualization","volume":"47","author":"Jendele","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022070423580055600_B30","doi-asserted-by":"crossref","first-page":"W413","DOI":"10.1093\/nar\/gkp281","article-title":"SITEHOUND-web: a server for ligand binding site identification in protein structures","volume":"37","author":"Hernandez","year":"2009","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W392\/44377222\/gkac323.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W392\/44377222\/gkac323.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,4]],"date-time":"2022-07-04T23:59:53Z","timestamp":1656979193000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/W1\/W392\/6582175"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,7]]},"references-count":30,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2022,5,7]]},"published-print":{"date-parts":[[2022,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac323","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"type":"print","value":"0305-1048"},{"type":"electronic","value":"1362-4962"}],"subject":[],"published-other":{"date-parts":[[2022,7,5]]},"published":{"date-parts":[[2022,5,7]]}}}