PDBe CCDUtils: an RDKit-based toolkit for handling and analysing small molecules in the Protein Data Bank

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...

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Veröffentlicht in:Journal of cheminformatics Jg. 15; H. 1; S. 117 - 11
Hauptverfasser: Kunnakkattu, Ibrahim Roshan, Choudhary, Preeti, Pravda, Lukas, Nadzirin, Nurul, Smart, Oliver S., Yuan, Qi, Anyango, Stephen, Nair, Sreenath, Varadi, Mihaly, Velankar, Sameer
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Cham Springer International Publishing 02.12.2023
BioMed Central Ltd
Springer Nature B.V
BMC
Schlagworte:
Annotations
Banks (Finance)
Bioinformatics
CCD
Chemistry
Chemistry and Materials Science
Computational Biology/Bioinformatics
Computational chemistry
Computer Applications in Chemistry
Data banks
Dictionaries
Documentation and Information in Chemistry
Informatics
Ligand
Ligands
Macromolecules
Molecular structure
PDB
Peptides
Physicochemical properties
Protein structure
Proteins
Python
RDKit
Software
Theoretical and Computational Chemistry
Toolkits
PRD
Ligand
CCD
BIRD
RDKit
CLC
PDBx/mmCIF
Protein structure
Covalently Linked Components
PDB
Python
ISSN:1758-2946, 1758-2946
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Beschreibung
Zusammenfassung: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
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ISSN:1758-2946
1758-2946
DOI:10.1186/s13321-023-00786-w