All-atom folding of the trp-cage protein with an adpative parallel tempering method

Forschungszentrum Karlsruhe, Institut für Nanotechnologie P.O. Box 3640, 76021 Karlsruhe, Germany

Received: 16 March 2004
Accepted: 5 May 2004

Abstract

Using the recently developed protein free-energy force field PFF01 we report the reproducible all-atom folding of the 20 amino acid trp-cage protein to within 2.0 backbone RMS deviation to the experimental structure with modest computational resources. We used an adapted version of the parallel tempering method as an inherently parallel stochastic optimization method. We find that near native structures dominate the low-energy spectrum of the final conformations and investigate the efficiency of the method as a function of the number of replicas in application to all-atom protein structure prediction.