AMBER Archive (2009)

Subject: [AMBER] PhD position in Computational Structural Biology at Cambridge, UK

From: Swanand Gore (
Date: Wed Jan 28 2009 - 04:31:16 CST

A PhD student position is available to develop new protein modelling methods
which can be applied to drug design. The successful candidate will work in
collaboration with the Blundell and Hyvonen groups in the Cambridge
University Biochemistry Department and industrial CASE award sponsors Eli

The optimization of a lead molecule in the early drug discovery process is
greatly accelerated by knowledge of the protein-ligand binding mode. However
it is not always possible to reliably predict this binding mode starting
from crystal structures of related proteins and ligands, due to the
conformational flexibility of the binding site. Inferring binding mode
becomes particularly hard for systems like GPCRs where there are substantial
difficulties in obtaining experimental protein-ligand structures. The
project will aim to develop a methodology for predicting binding modes by
combining approximate structural knowledge of the target with available
ligand activity data. The chosen student will work to extend the Rapper
program to use ligand-based pharmacophores as restraints in generating
feasible protein conformations, and to validate results on experimental

Applications should include a covering letter describing relevant research
experience to date, a CV, and the names and addresses of two referees. These
should be sent to Dr Mako Hyvonen (marko -at- by email
by 10th February 2009. Paper copies cannot be accepted.

This studentship is open to EU nationals only.

Limit of tenure: up to 3 years in first instance.
See also :

----Sent on behalf of Prof Tom Blundell and Dr Marko Hyvonen----
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