Ralf Schmid's Research Interests

Molecular Modelling, Bioinformatics, P2X receptors

Molecular Modelling and Bioinformatics

My research group has a broad interest in the application and development of computational methods covering different aspects of molecular modelling and bioinformatics.Techniques used in our lab are protein structure prediction by homology modelling and ab-initio modelling,  ligand docking and virtual screening, molecular dynamics simulations and free energy calculations, evolutionary analysis of protein families, and a range of bioinformatics methods.

A main focus is on understanding the molecular basis of P2X receptors activation and antagonism (in collaboration with Prof Evans' group, University of Leicester). P2X receptors are ligand-gated ion channels for Na+, K+ and Ca2+ activated by binding of extracellular ATP. The human genome encodes seven paralogous of the P2X receptor protein family (P2X1R-P2X7R) which form homo- and hetero-trimers. P2X receptors are involved in a variety of physiological and pathological processes, and particularly P2X7R is established as a drug target. For P2X7R we are interested in features that determine paralog specificity of steric and allosteric antagonists, and we have developed a robust protocol for predicitng binding poses of P2X7R antagonists. Other projects explore conformational changes occuring in the transition between different states of P2X receptors, and we calculate structural models for the P2X1R intracellular domain using ab-initio modelling informed by crosslinking derived constraints.

Other projects study the evolution of function and binding sites om protein families by phylogenetic analysis, use ligand docking and molecular dynamics simulations to investigate kinase activation and inhibition, develop methods for functional annotation of protein sequences, and study alternative splicing and its effects on protein structure based on RNAseq data.


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Contact Details

Department of Molecular and Cell Biology

T: +44(0)116 229 7038
E: MolCellBiol@le.ac.uk

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