Simulating virtual protein Calpha traces with applications

Abstract

We propose a simple procedure for generating virtual protein C(alpha) traces. One of the key ingredients of our method, to build a three-dimensional structure from a random sequence of amino acids, is to work directly on torsional angles of the chain which we sample from a von Mises distribution. With simple modeling of the hydrophobic effect in protein folding, the procedure produces compact and globular structures. Some characteristics of real proteins (i.e., compactness and globularity) are well mimicked by this procedure. These virtual traces are used to assess algorithms for matching protein structures or functional sites.