The CCDC has maintained internal research and collaborations in the field of protein structure and modelling and has co-developed a sophisticated database system for probing protein structure and protein-ligand interactions called Relibase. The high quality structural information available in the Cambridge Structural Database (CSD) can again be used to good effect when studying protein geometry and non-bonded interactions in proteins. Finding ways to use this information effectively is a primary research area for the CCDC. Other recent research includes the development of a novel secondary structure classification methodology and investigations into protein cavity similarities between non-homologous proteins. We also have a collaborative project to redesign enzymes to catalyse other non-biological chemical reactions such as the Diels-Alder reaction.

Research Plans

One research area is the development of methods to validate ligand models that are refined from X-ray data from protein-ligand complexes. Such models often appear highly strained and it is an important open question how much of this is due to errors in the refinement process and how much is truly low strain. Similarly, intermolecular interactions in proteins can be validated against CSD data. Another research interest is to develop knowledge based assessments of the quality of a ligand-protein interaction, which may prove more reliable than using other computational techniques. This can be used in approaches to predict the binding affinity of a given ligand.