The folding process defines three-dimensional protein structures from their amino acid chains. A protein's structure determines its activity and properties; thus knowing such conformation on an atomic level is essential for both basic and applied studies of protein function and dynamics. However, the acquisition of such structures by experimental methods is slow and expensive, and current computational methods mostly depend on previously known structures to determine new ones. Here we present a new software called GSAFold that applies the generalized simulated annealing (GSA) algorithm on ab initio protein structure prediction. The GSA is a stochastic search algorithm employed in energy minimization and used in global optimization problems, especially those that depend on long-range interactions, such as gravity models and conformation optimization of small molecules. This new implementation applies, for the first time in ab initio protein structure prediction, an analytical inverse for the Visitation function of GSA. It also employs the broadly used NAMD Molecular Dynamics package to carry out energy calculations, allowing the user to select different force fields and parameterizations. Moreover, the software also allows the execution of several simulations simultaneously. Applications that depend on protein structures include rational drug design and structure-based protein function prediction. Applying GSAFold in a test peptide, it was possible to predict the structure of mastoparan-X to a root mean square deviation of 3.00 Å.
Copyright © 2012 Wiley Periodicals, Inc.