{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T16:33:08Z","timestamp":1763224388915,"version":"3.45.0"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T00:00:00Z","timestamp":1740700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The Protein Data Bank (PDB) is an ever-growing database of three-dimensional macromolecular structures that has become a crucial resource for the drug discovery process. Exploring complexed proteins and accessing their associated ligands are essential for researchers to understand biological processes and design new compounds of pharmaceutical interest. However, currently available tools for large-scale ligand identification fail to address many of the more complex ways in which ligands are stored and represented in PDB structures. Therefore, a new tool called LigExtract was specifically developed for the large-scale processing of PDB structures and the identification of their ligands. This is a fully open-source tool available to the scientific community, designed to provide end-to-end processing. Users simply provide a list of UniProt IDs, and LigExtract returns a list of ligands, their individual PDB files, a PDB file of the protein chains interacting with the ligand, and a series of log files. These logs record the decisions made during the ligand extraction process and flag additional scenarios that might have to be considered during any follow-up use of the processed files (e.g., ligands covalently bound to the protein). LigExtract is freely available on GitHub (https:\/\/github.com\/comp-medchem\/LigExtract).<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf018","type":"journal-article","created":{"date-parts":[[2025,3,4]],"date-time":"2025-03-04T16:50:15Z","timestamp":1741107015000},"source":"Crossref","is-referenced-by-count":0,"title":["LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7039-0022","authenticated-orcid":false,"given":"Nat\u00e1lia","family":"Aniceto","sequence":"first","affiliation":[{"name":"Department of Pharmaceutical Sciences and Medicines, Faculdade de Farm\u00e1cia, Universidade de Lisboa , 1649-003 Lisboa,","place":["Portugal"]},{"name":"Research Institute for Medicines (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa , 1649-003 Lisboa,","place":["Portugal"]},{"name":"Department of Pharmacy, Phamacology and Health Technologies, Faculdade de Farm\u00e1cia, Universidade de Lisboa , 1649-003 Lisboa,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5102-4756","authenticated-orcid":false,"given":"Nuno","family":"Martinho","sequence":"additional","affiliation":[{"name":"Research Institute for Medicines (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa , 1649-003 Lisboa,","place":["Portugal"]},{"name":"iBB\u2500Institute for Bioengineering and Biosciences, Instituto Superior T\u00e9cnico, Universidade de Lisboa , 1049-001 Lisboa,","place":["Portugal"]},{"name":"Associate Laboratory i4HB\u2500Institute for Health and Bioeconomy at Instituto Superior T\u00e9cnico, Universidade de Lisboa , 1049-001 Lisboa,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3718-3264","authenticated-orcid":false,"given":"Ismael","family":"Rufino","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences and Medicines, Faculdade de Farm\u00e1cia, Universidade de Lisboa , 1649-003 Lisboa,","place":["Portugal"]},{"name":"Research Institute for Medicines (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa , 1649-003 Lisboa,","place":["Portugal"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5790-9181","authenticated-orcid":false,"given":"Rita C","family":"Guedes","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences and Medicines, Faculdade de Farm\u00e1cia, Universidade de Lisboa , 1649-003 Lisboa,","place":["Portugal"]},{"name":"Research Institute for Medicines (iMed.ULisboa), Faculdade de Farm\u00e1cia, Universidade de Lisboa , 1649-003 Lisboa,","place":["Portugal"]}]}],"member":"286","published-online":{"date-parts":[[2025,2,28]]},"reference":[{"key":"2025111511272020900_qzaf018-B1","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":"2025111511272020900_qzaf018-B2","doi-asserted-by":"crossref","first-page":"e1006483","DOI":"10.1371\/journal.pcbi.1006483","article-title":"A benchmark driven guide to binding site comparison: an exhaustive evaluation using tailor-made data sets (ProSPECCTs)","volume":"14","author":"Ehrt","year":"2018","journal-title":"PLoS Comput Biol"},{"key":"2025111511272020900_qzaf018-B3","doi-asserted-by":"crossref","first-page":"2356","DOI":"10.1021\/acs.jcim.9b00554","article-title":"DeeplyTough: learning structural comparison of protein binding sites","volume":"60","author":"Simonovsky","year":"2020","journal-title":"J Chem Inf Model"},{"key":"2025111511272020900_qzaf018-B4","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1039\/C9MD00102F","article-title":"Binding site characterization \u2013 similarity, promiscuity, and druggability","volume":"10","author":"Ehrt","year":"2019","journal-title":"Medchemcomm"},{"key":"2025111511272020900_qzaf018-B5","doi-asserted-by":"crossref","first-page":"e1007864","DOI":"10.1371\/journal.pcbi.1007864","article-title":"Sequence-based prediction of protein binding mode landscapes","volume":"16","author":"Horvath","year":"2020","journal-title":"PLoS Comput Biol"},{"key":"2025111511272020900_qzaf018-B6","doi-asserted-by":"crossref","first-page":"D562","DOI":"10.1093\/nar\/gkaa895","article-title":"KLIFS: an overhaul after the first 5 years of supporting kinase research","volume":"49","author":"Kanev","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B7","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.str.2018.02.001","article-title":"An augmented pocketome: detection and analysis of small-molecule binding pockets in proteins of known 3D structure","volume":"26","author":"Bhagavat","year":"2018","journal-title":"Structure"},{"key":"2025111511272020900_qzaf018-B8","doi-asserted-by":"crossref","first-page":"W48","DOI":"10.1093\/nar\/gkaa235","article-title":"ProteinsPlus: interactive analysis of protein\u2013ligand binding interfaces","volume":"48","author":"Sch\u00f6ning-Stierand","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B9","doi-asserted-by":"crossref","first-page":"D399","DOI":"10.1093\/nar\/gku928","article-title":"sc-PDB: a 3D-database of ligandable binding sites\u201410 years on","volume":"43","author":"Desaphy","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B10","doi-asserted-by":"crossref","first-page":"2423","DOI":"10.1016\/j.jmb.2019.05.024","article-title":"Updates to Binding MOAD (mother of all databases): polypharmacology tools and their utility in drug repurposing","volume":"431","author":"Smith","year":"2019","journal-title":"J Mol Biol"},{"key":"2025111511272020900_qzaf018-B11","doi-asserted-by":"crossref","first-page":"594","DOI":"10.1126\/science.aaf8993","article-title":"The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design","volume":"353","author":"Schrader","year":"2016","journal-title":"Science"},{"key":"2025111511272020900_qzaf018-B12","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1002\/cmdc.201700505","article-title":"IChem: a versatile toolkit for detecting, comparing, and predicting protein\u2013ligand interactions","volume":"13","author":"Da Silva","year":"2018","journal-title":"ChemMedChem"},{"key":"2025111511272020900_qzaf018-B13","doi-asserted-by":"crossref","first-page":"D674","DOI":"10.1093\/nar\/gkm911","article-title":"Binding MOAD, a high-quality protein\u2013ligand database","volume":"36","author":"Benson","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B14","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1093\/bioinformatics\/btu789","article-title":"The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank","volume":"31","author":"Westbrook","year":"2015","journal-title":"Bioinformatics"},{"key":"2025111511272020900_qzaf018-B15","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/1758-2946-6-12","article-title":"Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes","volume":"6","author":"Bietz","year":"2014","journal-title":"J Cheminform"},{"key":"2025111511272020900_qzaf018-B16","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1186\/1758-2946-1-13","article-title":"Fast automated placement of polar hydrogen atoms in protein-ligand complexes","volume":"1","author":"Lippert","year":"2009","journal-title":"J Cheminform"},{"key":"2025111511272020900_qzaf018-B17","doi-asserted-by":"crossref","first-page":"W443","DOI":"10.1093\/nar\/gkv315","article-title":"PLIP: fully automated protein\u2013ligand interaction profiler","volume":"43","author":"Salentin","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B18","doi-asserted-by":"crossref","first-page":"W530","DOI":"10.1093\/nar\/gkab294","article-title":"PLIP 2021: expanding the scope of the protein\u2013ligand interaction profiler to DNA and RNA","volume":"49","author":"Adasme","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B19","doi-asserted-by":"crossref","first-page":"D1096","DOI":"10.1093\/nar\/gks966","article-title":"BioLiP: a semi-manually curated database for biologically relevant ligand\u2013protein interactions","volume":"41","author":"Yang","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B20","doi-asserted-by":"crossref","first-page":"D404","DOI":"10.1093\/nar\/gkad630","article-title":"BioLiP2: an updated structure database for biologically relevant ligand\u2013protein interactions","volume":"52","author":"Zhang","year":"2024","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B21","doi-asserted-by":"crossref","first-page":"2153","DOI":"10.1093\/bioinformatics\/bth214","article-title":"Ligand Depot: a data warehouse for ligands bound to macromolecules","volume":"20","author":"Feng","year":"2004","journal-title":"Bioinformatics"},{"key":"2025111511272020900_qzaf018-B22","doi-asserted-by":"crossref","first-page":"W337","DOI":"10.1093\/nar\/gkx333","article-title":"ProteinsPlus: a web portal for structure analysis of macromolecules","volume":"45","author":"F\u00e4hrrolfes","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2025111511272020900_qzaf018-B23","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.str.2021.10.003","article-title":"Simplified quality assessment for small-molecule ligands in the Protein Data Bank","volume":"30","author":"Shao","year":"2022","journal-title":"Structure"},{"key":"2025111511272020900_qzaf018-B24","doi-asserted-by":"crossref","first-page":"317","DOI":"10.1038\/nrd.2018.14","article-title":"Unexplored therapeutic opportunities in the human genome","volume":"17","author":"Oprea","year":"2018","journal-title":"Nat Rev Drug Discov"},{"key":"2025111511272020900_qzaf018-B25","doi-asserted-by":"crossref","first-page":"659","DOI":"10.1002\/bip.22434","article-title":"Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank","volume":"101","author":"Dutta","year":"2014","journal-title":"Biopolymers"},{"key":"2025111511272020900_qzaf018-B26","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1186\/s12859-023-05388-9","article-title":"BeEM: fast and faithful conversion of mmCIF format structure files to PDB format","volume":"24","author":"Zhang","year":"2023","journal-title":"BMC Bioinformatics"},{"key":"2025111511272020900_qzaf018-B27","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1016\/S0022-0248(98)00852-5","article-title":"Additives for the crystallization of proteins and nucleic acids","volume":"196","author":"Sauter","year":"1999","journal-title":"J Cryst Growth"},{"key":"2025111511272020900_qzaf018-B28","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1038\/nprot.2007.198","article-title":"Crystallization of soluble proteins in vapor diffusion for x-ray crystallography","volume":"2","author":"Benvenuti","year":"2007","journal-title":"Nat Protoc"},{"key":"2025111511272020900_qzaf018-B29","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1021\/acsomega.9b02697","article-title":"Computational analysis of crystallization additives for the identification of new allosteric sites","volume":"5","author":"Fogha","year":"2020","journal-title":"ACS Omega"},{"author":"Hampton Research","key":"2025111511272020900_qzaf018-B30"},{"year":"1997","author":"Glasgow University Protein Crystallography","key":"2025111511272020900_qzaf018-B31"},{"first-page":"11","year":"2008","author":"Hagberg","key":"2025111511272020900_qzaf018-B32"},{"key":"2025111511272020900_qzaf018-B33","doi-asserted-by":"crossref","first-page":"4592","DOI":"10.1038\/s41467-021-24866-3","article-title":"PALI1 facilitates DNA and nucleosome binding by PRC2 and triggers an allosteric activation of catalysis","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat Commun"},{"key":"2025111511272020900_qzaf018-B34","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/S1074-5521(00)00104-6","article-title":"Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator","volume":"7","author":"Katz","year":"2000","journal-title":"Chem Biol"},{"key":"2025111511272020900_qzaf018-B35","doi-asserted-by":"crossref","first-page":"25638","DOI":"10.1074\/jbc.M113.494955","article-title":"Structural insights into central hypertension regulation by human aminopeptidase A","volume":"288","author":"Yang","year":"2013","journal-title":"J Biol Chem"},{"key":"2025111511272020900_qzaf018-B36","doi-asserted-by":"crossref","first-page":"279","DOI":"10.21105\/joss.00279","article-title":"BioPandas: working with molecular structures in pandas DataFrames","volume":"2","author":"Raschka","year":"2017","journal-title":"J Open Source Softw"}],"container-title":["Genomics, Proteomics &amp; Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gpb\/advance-article-pdf\/doi\/10.1093\/gpbjnl\/qzaf018\/62204298\/qzaf018.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/23\/4\/qzaf018\/62204298\/qzaf018.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gpb\/article-pdf\/23\/4\/qzaf018\/62204298\/qzaf018.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,15]],"date-time":"2025-11-15T16:27:32Z","timestamp":1763224052000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gpb\/article\/doi\/10.1093\/gpbjnl\/qzaf018\/8046017"}},"subtitle":[],"editor":[{"given":"Xin","family":"Gao","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2025,2,28]]},"references-count":36,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,9,22]]}},"URL":"https:\/\/doi.org\/10.1093\/gpbjnl\/qzaf018","relation":{},"ISSN":["1672-0229","2210-3244"],"issn-type":[{"type":"print","value":"1672-0229"},{"type":"electronic","value":"2210-3244"}],"subject":[],"published-other":{"date-parts":[[2025,8]]},"published":{"date-parts":[[2025,2,28]]},"article-number":"qzaf018"}}