All‐atom folding of the three‐helix HIV accessory protein with an adaptive parallel tempering method

All‐atom protein structure prediction from the amino acid sequence alone remains an important goal of biophysical chemistry. Recent progress in force field development and validation suggests that the PFF01 free‐energy force field correctly predicts the native conformation of various helical proteins as the global optimum of its free‐energy surface. Reproducible protein structure prediction requires the availability of efficient optimization methods to locate the global minima of such complex potentials. Here we investigate an adapted version of the parallel tempering method as an efficient parallel stochastic optimization method for protein structure prediction. Using this approach we report the reproducible all‐atom folding of the three‐helix 40 amino acid HIV accessory protein from random conformations to within 2.4 Å backbone RMS deviation from the experimental structure with modest computational resources. Proteins 2004. © 2004 Wiley‐Liss, Inc.

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