Genome-wide Structure Prediction of Globular and Transmembrane Helical Proteins

University Of California-Berkeley, Berkeley CA

Investigators

Abstract

Prediction of protein structure based on sequence information is of great value for the interpretation of genomic sequence data. Such method would reduce the number of protein structure that must be determined experimentally to obtain a structural complement for an organism. The new method integrates tools such as secondary structure prediction and distance-based torsion angle dynamics with the idea of patch-based tertiary contact prediction and bootstrapping. The first class of proteins will be those that take on an alpha-helical structure, the class of proteins for which prediction has been most successful. The method will be extended to predict arrangements of transmembrane helices. A further extension to the structure of beta-sheet proteins will involve motif detection and accumulation of motifs into larger structures. The methods will be optimized and scored to aid in selecting the best model structure. The result will be automated high accuracy software that can be used on whole genome sequences.