Generating ensemble averages for small proteins from extended conformations by Monte Carlo simulations.
Since it is not feasible to determine the structure of every protein by experiment, algorithms delivering the folded conformation of a protein solely from its amino acid sequence are desirable. Here the diffusion-process controlled-Monte Carlo approach has been applied to generating ensemble averages for three small proteins with 31, 36, and 46 residues. Starting from extended conformations and using an energy model that was developed on other protein models, the simulations find nativelike structures deviating by 3 A rms from the experimental structures for the main chain atoms. The balance between long-range and short-range interactions is discussed briefly in the context of stability and folding.
Derreumaux
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Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
D003198:Computer Simulation; D008956:Models, Chemical; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D010455:Peptides