Exploiting co-evolution across many protein families for predicting native contacts

by Andrea Pagnani (Human Genetic Foundation-Torino)

Wednesday 28 Sept 2011, 15:00 → 17:00 Europe/Rome

Aula Careri (Dip. di Fisica - Edificio G. Marconi)

Correlated substitution patterns between residues of a protein family have been exploited to reveal information on the structures of proteins However, such studies require a large number (e.g., the order of one thousand) of homologous yet variable protein sequences. Most studies so far have been limited to a few exemplary proteins for which a large number of such sequences happen to be available. Rapid advances in genome sequencing will soon be able to generate this many sequences for the majority of common bacterial proteins. Sequencing a large number of simple eukaryotes such as yeast can in principle generate similar number of common eukaryotic protein sequences, beyond a collection of highly amplified protein domains which already reach the necessary numbers. In this seminar I will provide a systematic evaluation of the information contained in correlated substitution patterns for predicting residue contacts, a first step towards a purely sequence-based approach to protein structure prediction, and an introduction to the inference method we have developed.