PDBe Graph Database: A Neo4J-driven integrative knowledge graph for structural data


 Wednesday 27 May 202015:30 (Europe/London)


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Ajay Mishra

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This webinar will introduce the concepts of a graph database and describe how we used a graph-approach for integrating the structural data of the Protein Data Bank.

The presented PDBe knowledge graph combines annotations provided by PDBe-KB partners with the core PDB archive. Each PDB entry can be thought of as a tree, with the root being the PDB entry, connected to chains and entities, which are then connected to residues. Each of the more than 150 million PDB residues, the leaves of the tree representation, are linked to annotations that make it easier to answer scientific questions such as: Can we find small molecules which have the same scaffold, and interact with the same binding sites? Or, can we find macromolecular interaction interfaces which have highly conserved residues, and are annotated to be structurally flexible?

The webinar will help the audience answer these, and other similar scientific questions and will provide a solid foundation for taking advantage of the PDBe knowledge graph and use it as an invaluable research tool.

This webinar took place on 27 May 2020. You can watch a recording and download the slides in Train online.


This webinar is best suited for bioinformaticians with some experience in analysing structural data from the PDB using programmatic and/or high-throughput data access.