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Here, we present PDBe CCDUtils, a versatile toolkit for processing and analysing small molecules from the PDB in PDBx\/mmCIF format. PDBe CCDUtils provides streamlined access to all the metadata for small molecules in the PDB and offers a set of convenient methods to compute various properties using RDKit, such as 2D depictions, 3D conformers, physicochemical properties, scaffolds, common fragments, and cross-references to small molecule databases using UniChem. The toolkit also provides methods for identifying all the covalently attached chemical components in a macromolecular structure and calculating similarity among small molecules. By providing a broad range of functionality, PDBe CCDUtils caters to the needs of researchers in cheminformatics, structural biology, bioinformatics and computational chemistry.<\/jats:p>\n                  <jats:p>\n                    <jats:bold>Graphical Abstract<\/jats:bold>\n                  <\/jats:p>","DOI":"10.1186\/s13321-023-00786-w","type":"journal-article","created":{"date-parts":[[2023,12,2]],"date-time":"2023-12-02T00:01:58Z","timestamp":1701475318000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank"],"prefix":"10.1186","volume":"15","author":[{"given":"Ibrahim Roshan","family":"Kunnakkattu","sequence":"first","affiliation":[]},{"given":"Preeti","family":"Choudhary","sequence":"additional","affiliation":[]},{"given":"Lukas","family":"Pravda","sequence":"additional","affiliation":[]},{"given":"Nurul","family":"Nadzirin","sequence":"additional","affiliation":[]},{"given":"Oliver S.","family":"Smart","sequence":"additional","affiliation":[]},{"given":"Qi","family":"Yuan","sequence":"additional","affiliation":[]},{"given":"Stephen","family":"Anyango","sequence":"additional","affiliation":[]},{"given":"Sreenath","family":"Nair","sequence":"additional","affiliation":[]},{"given":"Mihaly","family":"Varadi","sequence":"additional","affiliation":[]},{"given":"Sameer","family":"Velankar","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,12,2]]},"reference":[{"key":"786_CR1","doi-asserted-by":"publisher","first-page":"D520","DOI":"10.1093\/nar\/gky949","volume":"47","author":"SK Burley","year":"2019","unstructured":"wwPDB consortium, Burley SK, Berman HM, et al (2019) Protein Data Bank: the single global archive for 3D macromolecular structure data. 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