{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T17:38:29Z","timestamp":1787765909378,"version":"build-2784847793"},"reference-count":18,"publisher":"Wiley","issue":"12","license":[{"start":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T00:00:00Z","timestamp":1762905600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"},{"start":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T00:00:00Z","timestamp":1762905600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[2025,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The Protein Data Bank (PDB) contains more than 235,000 three\u2010dimensional biostructures and is growing at a rate of nearly 10% per year. The PDB is essential to gain knowledge on how proteins and ligands interact and how these interactions are correlated with the quantitative activity of each ligand\/target pair. Unfortunately, the lack of a tool that can classify structures as apo or holo, that is by no means straightforward, and differentiate between covalent and non\u2010covalent ligand\u2013protein complexes makes it difficult to obtain the structures that belong to each set. To address this issue, we present PDB\u2010CAT, a user\u2010friendly tool that facilitates the categorization and extraction of key information from PDBx\/mmCIF files through an efficient parallelized implementation. PDB\u2010CAT uses a blacklist\u2010based approach to automatically identify the ligand in a complex. It then classifies the PDB files based on ligand presence: structures without a ligand are classified as apo, whereas those with a ligand are classified as covalently or non\u2010covalently bound, depending on the type of binding. As well as making this classification, the program can verify if there are any mutations in the protein sequence by comparing it to a reference sequence. An example is included to illustrate two different uses: the classification of SARS\u2010CoV\u20102 Main Protease complexes depending on their variant, and the complete screening of the PDBbindv2020, achieved in &lt;10\u2009min. PDB\u2010CAT is now available on GitHub (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/github.com\/URV-cheminformatics\/PDB-CAT\">https:\/\/github.com\/URV-cheminformatics\/PDB-CAT<\/jats:ext-link>\n                    ) and the corresponding tutorial on GitBook (\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/ariadnallopps-organization.gitbook.io\/pdb-cat\">https:\/\/ariadnallopps-organization.gitbook.io\/pdb-cat<\/jats:ext-link>\n                    ).\n                  <\/jats:p>","DOI":"10.1002\/pro.70379","type":"journal-article","created":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T07:45:27Z","timestamp":1763019927000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["<scp>PDB<\/scp>\n                    \u2010\n                    <scp>CAT<\/scp>\n                    : A user\u2010friendly tool to classify and analyze\n                    <scp>PDB<\/scp>\n                    protein\u2013ligand complexes"],"prefix":"10.1002","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-9785-3852","authenticated-orcid":false,"given":"Ariadna","family":"Llop\u2010Peir\u00f3","sequence":"first","affiliation":[{"name":"Departament de Bioqu\u00edmica i Biotecnologia, Research Group in Cheminformatics &amp; Nutrition Universitat Rovira i Virgili  Tarragona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Said","family":"Trujillo\u2010De Le\u00f3n","sequence":"additional","affiliation":[{"name":"Departament de Bioqu\u00edmica i Biotecnologia, Research Group in Cheminformatics &amp; Nutrition Universitat Rovira i Virgili  Tarragona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2598-8089","authenticated-orcid":false,"given":"Gerard","family":"Pujadas","sequence":"additional","affiliation":[{"name":"Departament de Bioqu\u00edmica i Biotecnologia, Research Group in Cheminformatics &amp; Nutrition Universitat Rovira i Virgili  Tarragona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0348-7497","authenticated-orcid":false,"given":"Santiago","family":"Garcia\u2010Vallv\u00e9","sequence":"additional","affiliation":[{"name":"Departament de Bioqu\u00edmica i Biotecnologia, Research Group in Cheminformatics &amp; Nutrition Universitat Rovira i Virgili  Tarragona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7654-6689","authenticated-orcid":false,"given":"Aleix","family":"Gimeno","sequence":"additional","affiliation":[{"name":"Departament de Bioqu\u00edmica i Biotecnologia, Research Group in Cheminformatics &amp; Nutrition Universitat Rovira i Virgili  Tarragona Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2025,11,12]]},"reference":[{"key":"e_1_2_9_2_1","doi-asserted-by":"publisher","DOI":"10.1039\/d0cs01118e"},{"key":"e_1_2_9_3_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1077"},{"key":"e_1_2_9_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp163"},{"key":"e_1_2_9_5_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20061375"},{"key":"e_1_2_9_6_1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules20021984"},{"key":"e_1_2_9_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.drudis.2024.104137"},{"key":"e_1_2_9_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/med.21862"},{"key":"e_1_2_9_9_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23010259"},{"key":"e_1_2_9_10_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-biochem-030222-120000"},{"key":"e_1_2_9_11_1","unstructured":"RCSB PDB.PDB statistics: Overall growth of released structures per year. The RCSB Protein Data Bank.2024ahttps:\/\/www.rcsb.org\/stats\/growth\/growth-released-structures"},{"key":"e_1_2_9_12_1","unstructured":"RCSB PDB.Beginner's guide to PDB structures and the PDBx\/mmCIF format.2024bhttps:\/\/pdb101.rcsb.org\/learn\/guide\u2010to\u2010understanding\u2010pdb\u2010data\/beginner%E2%80%99s\u2010guide\u2010to\u2010pdbx\u2010mmcif"},{"key":"e_1_2_9_13_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41422-022-00640-y"},{"key":"e_1_2_9_14_1","doi-asserted-by":"publisher","DOI":"10.3390\/ijms24109072"},{"key":"e_1_2_9_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-021-04271-9"},{"key":"e_1_2_9_16_1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules25204723"},{"key":"e_1_2_9_17_1","doi-asserted-by":"publisher","DOI":"10.1021\/jm030580l"},{"key":"e_1_2_9_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2023.11.009"},{"key":"e_1_2_9_19_1","doi-asserted-by":"publisher","DOI":"10.3390\/molecules27144568"}],"container-title":["Protein Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.70379","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/pro.70379","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/pro.70379","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T05:19:54Z","timestamp":1775884794000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.70379"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,12]]},"references-count":18,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["10.1002\/pro.70379"],"URL":"https:\/\/doi.org\/10.1002\/pro.70379","archive":["Portico"],"relation":{"has-preprint":[{"id-type":"doi","id":"10.26434\/chemrxiv-2024-54073","asserted-by":"object"}]},"ISSN":["0961-8368","1469-896X"],"issn-type":[{"value":"0961-8368","type":"print"},{"value":"1469-896X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,12]]},"assertion":[{"value":"2025-07-02","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-10-29","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2025-11-12","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e70379"}}