Projects

PDBe-KB Ligands

An interactive webpage to explore the structures of ligands in the PDB including their substructures and fragments, physicochemcial properties, and interactions with proteins.

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PDBe Arpeggio

A Python package for calculating interatomic interactions in biomacromolecules. Supports 15 interaction subtypes and works with protein-ligand, protein-protein, and nucleic acid interactions.

Code

PDBe CCDUtils

An open-source Python toolkit for processing small molecule data in the PDB. Parses CIF files and converts them to RDKit mol objects for easy analysis.

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PDBe RelLig

Automatically annotates the biological role of ligands in the PDB. Distinguishes between biologically relevant molecules and those present for experimental purposes.

Code