While the Protein Data Bank (PDB) contains a wealth of structural information on ligands bound to macromolecules, their analysis can be challenging due to the large amount and diversity of data. 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. Graphical Abstract: [Figure not available: see fulltext.].
CITATION STYLE
Kunnakkattu, I. R., Choudhary, P., Pravda, L., Nadzirin, N., Smart, O. S., Yuan, Q., … Velankar, S. (2023). PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank. Journal of Cheminformatics, 15(1). https://doi.org/10.1186/s13321-023-00786-w
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