The University of Southampton
Chemistry

Research project: Skylaris: Biological Simulations

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By combining large-scale first principles quantum mechanical calculations with molecular dynamics simulations we have a powerful approach for studying a variety of problems involving biological molecules.

Project Overview

By combining large-scale first principles quantum mechanical calculations with molecular dynamics simulations we can study the dynamical behaviour of biomolecules as well as the electronic polarization and charge transfer that determine all the interactions, including chemical bond formation. The ability to accurately describe all these effects is a requirement for the rational development of new drugs or the understanding of catalysis in enzymes. We are developing such techniques in order to calculate free energies of binding of ligands to proteins and transition states and activation energies for catalytic reactions in enzymes.

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Figure: A 5700-atom protein in cartoon representation. The ligand binding pocket is shown as well as a contour of the electronic density of the entire protein.

Related research groups

Computational Systems Chemistry

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