{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,1]],"date-time":"2026-03-01T09:18:22Z","timestamp":1772356702641,"version":"3.50.1"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,25]],"date-time":"2022-05-25T00:00:00Z","timestamp":1653436800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"ELIXIR CZ Research Infrastructure","award":["LM2018131"],"award-info":[{"award-number":["LM2018131"]}]},{"name":"ELIXIR CZ Research Infrastructure","award":["MEYS CR"],"award-info":[{"award-number":["MEYS CR"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Knowledge of protein\u2013ligand binding sites (LBSs) enables research ranging from protein function annotation to structure-based drug design. To this end, we have previously developed a stand-alone tool, P2Rank, and the web server PrankWeb (https:\/\/prankweb.cz\/) for fast and accurate LBS prediction. Here, we present significant enhancements to PrankWeb. First, a new, more accurate evolutionary conservation estimation pipeline based on the UniRef50 sequence database and the HMMER3 package is introduced. Second, PrankWeb now allows users to enter UniProt ID to carry out LBS predictions in situations where no experimental structure is available by utilizing the AlphaFold model database. Additionally, a range of minor improvements has been implemented. These include the ability to deploy PrankWeb and P2Rank as Docker containers, support for the mmCIF file format, improved public REST API access, or the ability to batch download the LBS predictions for the whole PDB archive and parts of the AlphaFold database.<\/jats:p>","DOI":"10.1093\/nar\/gkac389","type":"journal-article","created":{"date-parts":[[2022,5,6]],"date-time":"2022-05-06T11:36:33Z","timestamp":1651836993000},"page":"W593-W597","source":"Crossref","is-referenced-by-count":167,"title":["PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures"],"prefix":"10.1093","volume":"50","author":[{"given":"David","family":"Jakubec","sequence":"first","affiliation":[{"name":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University , Czech Republic"}]},{"given":"Petr","family":"Skoda","sequence":"additional","affiliation":[{"name":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University , Czech Republic"}]},{"given":"Radoslav","family":"Krivak","sequence":"additional","affiliation":[{"name":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University , Czech Republic"}]},{"given":"Marian","family":"Novotny","sequence":"additional","affiliation":[{"name":"Department of Cell Biology, Faculty of Science, Charles University , Czech Republic"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4679-0557","authenticated-orcid":false,"given":"David","family":"Hoksza","sequence":"additional","affiliation":[{"name":"Department of Software Engineering, Faculty of Mathematics and Physics, Charles University , Czech Republic"}]}],"member":"286","published-online":{"date-parts":[[2022,5,24]]},"reference":[{"key":"2023071818180791100_B1","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1186\/s13321-015-0096-0","article-title":"Modeling enzyme-ligand binding in drug discovery","volume":"7","author":"Konc","year":"2015","journal-title":"J. Cheminform."},{"key":"2023071818180791100_B2","doi-asserted-by":"crossref","first-page":"1837","DOI":"10.1038\/s41467-020-15611-3","article-title":"Allosteric regulation accompanied by oligomeric state changes of Trypanosoma brucei GMP reductase through cystathionine-\u03b2-synthase domain","volume":"11","author":"Imamura","year":"2020","journal-title":"Nat. Commun."},{"key":"2023071818180791100_B3","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1186\/s13321-018-0285-8","article-title":"P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure","volume":"10","author":"Kriv\u00e1k","year":"2018","journal-title":"J. Cheminf."},{"key":"2023071818180791100_B4","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1093\/bioinformatics\/btab009","article-title":"DeepSurf: a surface-based deep learning approach for the prediction of ligand binding sites on proteins","volume":"37","author":"Mylonas","year":"2021","journal-title":"Bioinformatics"},{"key":"2023071818180791100_B5","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":"2023071818180791100_B6","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023071818180791100_B7","first-page":"D570","article-title":"MGnify: the microbiome analysis resource in 2020","volume":"48","author":"Mitchell","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2023071818180791100_B8","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"2023071818180791100_B9","doi-asserted-by":"crossref","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"2023071818180791100_B10","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1093\/bioinformatics\/btm270","article-title":"Predicting functionally important residues from sequence conservation","volume":"23","author":"Capra","year":"2007","journal-title":"Bioinformatics"},{"key":"2023071818180791100_B11","doi-asserted-by":"crossref","first-page":"W15","DOI":"10.1093\/nar\/gkab377","article-title":"Amino Acid Interactions (INTAA) web server v2.0: a single service for computation of energetics and conservation in biomolecular 3D structures","volume":"49","author":"Vym\u011btal","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023071818180791100_B12","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1093\/bioinformatics\/btu739","article-title":"UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches","volume":"31","author":"Suzek","year":"2015","journal-title":"Bioinformatics"},{"key":"2023071818180791100_B13","doi-asserted-by":"crossref","first-page":"1067","DOI":"10.1016\/0022-2836(94)90012-4","article-title":"Volume changes in protein evolution","volume":"236","author":"Gerstein","year":"1994","journal-title":"J. Mol. Biol."},{"key":"2023071818180791100_B14","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/s41392-020-00435-w","article-title":"G protein-coupled receptors: structure- and function-based drug discovery","volume":"6","author":"Yang","year":"2021","journal-title":"Signal Transduct. Target Ther."},{"key":"2023071818180791100_B15","doi-asserted-by":"crossref","first-page":"22","DOI":"10.3389\/fendo.2012.00022","article-title":"The succinate receptor as a novel therapeutic target for oxidative and metabolic stress-related conditions","volume":"3","author":"Ariza","year":"2012","journal-title":"Front. Endocrinol. (Lausanne)"},{"key":"2023071818180791100_B16","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nature13083","article-title":"Structure of the human P2Y12 receptor in complex with an antithrombotic drug","volume":"509","author":"Zhang","year":"2014","journal-title":"Nature"}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W593\/50907588\/gkac389.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/W1\/W593\/50907588\/gkac389.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,18]],"date-time":"2023-07-18T18:19:42Z","timestamp":1689704382000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/W1\/W593\/6591527"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,5,24]]},"references-count":16,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2022,5,24]]},"published-print":{"date-parts":[[2022,7,5]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac389","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,7,5]]},"published":{"date-parts":[[2022,5,24]]}}}