We examine by a molecular simulation whether or not the transmembrane helices of bacteriorhodopsin have the ability to self-assemble into the native configuration by themselves. Starting from random initial configurations of seven transmembrane helices, the same helix arrangement as the experimental one (PDB code: IC3W) was obtained by a replica-exchange Monte Carlo simulation. This implies that helix-helix interactions are the main driving force for the native structure formation of bacteriorhodopsin. (C) 2004 Elsevier B.V. All rights reserved.