Stochastic optimization methods for biomolecular structure prediction

Abstract

Protein structure prediction (PSP) remains one of the main outstanding challenges of theoretical biophysical chemistry. Its goal is to predict the fully three-dimensional tertiary structure of the protein on the basis of its amino acid sequence alone. Here we report on the development of a. specific biomolecular forcefield with an implicit solvent model and novel simulation methods that enhance the simulation speed by several orders of magnitude. We report on the progress of two folding studies for the 36 amino-acid avian pancreatic polypeptide (1PPT) and the 42 amino-acid headgroup of the HIV-1 accessory protein (1F4I).