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ELIXIR | 3D-Bioinfo: Integrating structural and functional data to support in silico predictions in drug design


Thursday, 3rd September


13:30 to 16:30 (CEST)

Instructors and helpers 

  • Christine Orengo | University College London (UCL), United Kingdom
  • Preeti Choudhary | Protein Data Bank in Europe (PDBe), United Kingdom
  • Vincent Zoete | University of Lausanne (UNIL), Switzerland


The 3D-BioInfo Community aims to increase interoperability between resources by developing and promoting data standards, integrating data where appropriate and developing robust benchmarking strategies for prediction algorithms (e.g. protein structures, complexes, ligand/drug docking). Two major activities are the integration of known and predicted functional site data (e.g. ligand binding and protein interface residues) and protein ligand docking. In the first part of this tutorial students will be taught how to access the site data in the PDBe Knowledge Base. The second part will then cover protein ligand interactions and drug design.

Target audience

Attendees with an interest in finding and understanding functional information related to macromolecular structures and drug binding sites. Attendees should have a basic knowledge of biology and very basic knowledge of chemistry.

Maximum participants

This tutorial is open to at most 20 attendees.


Computer with UCSF Chimera installed and a web browser (recent version of Firefox or Chrome).


Time (CEST)
13:30 - 14:30 Introduction to the 3D-BioInfo Community and available proteins structure and function annotations - Christine Orengo
14:30 - 15:30 Introduction to the Protein Data Bank in Europe Knowledge Base (PDBe-KB) resource and the aggregated views of proteins. Demonstration of the visualization tools in these pages and how they can be used to identify important functional sites - David Armstrong
15:30 - 16:30 Introduction to molecular interactions in binding of drug-like ligands, followed by a tutorial on UCSF Chimera and docking tools - Vincent Zoete