| Autor: |
Ibrahim Roshan Kunnakkattu, Preeti Choudhary, Lukas Pravda, Nurul Nadzirin, Oliver S. Smart, Qi Yuan, Stephen Anyango, Sreenath Nair, Mihaly Varadi, Sameer Velankar |
| Jazyk: |
angličtina |
| Rok vydání: |
2023 |
| Předmět: |
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| Zdroj: |
Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-11 (2023) |
| Druh dokumentu: |
article |
| ISSN: |
1758-2946 |
| DOI: |
10.1186/s13321-023-00786-w |
| Popis: |
Abstract 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 |
| Databáze: |
Directory of Open Access Journals |
| Externí odkaz: |
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