PDBe-KB - enhancing impact of structural knowledgebase in basic and translational research with focus on Pathogenic Mutations


  • Dr Sameer Velankar

    European Molecular Biology Laboratory, United Kingdom

  • Prof Christine Orengo

    University College London, United Kingdom

  • Dr Alexey Murzin

    MRC Laboratory of Molecular Biology, United Kingdom

  • Dr Robert Finn

    European Bioinformatics Institute, United Kingdom

  • Prof Julian Gough

    MRC Laboratory of Molecular Biology, United Kingdom

Project summary

In biology, the form or three-dimensional (3D) macromolecular protein structure dictates function. To date >175,000 experimentally determined 3D structures have been archived in the Protein Data Bank (PDB). Recent advances in structure prediction complement the data available in the PDB with predicted 3D-models. The PDBe-KnowledgeBase (PDBe-KB) is a world-leading, community-driven resource that integrates experimental structures from the PDB, predicted 3D-models from world-leading resources and enhances these structures with functional annotations (e.g. predicted functional sites, residue mutation impacts) from niche data resources in a comprehensive knowledge graph to facilitate explorations of fundamental biology, biomedicine, biotechnology, bioenergy, and STEM education about proteins, in 3D. The 3D-structure data is being used to illuminate the consequences of variation in SARS-CoV-2. This project will expand the data in PDBe-KB establishing a comprehensive 3D-fold structure domain library with the goal of significantly increasing structure coverage for sequences with particular focus on proteins from human and pathogens.