The FASEB Journal, Vol 10, 119-125, Copyright © 1996 by The Federation of American Societies for Experimental Biology

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Protein folding by a biased Monte Carlo procedure in the dihedral angle space

B Lee, N Kurochkina and HS Kang
Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.

A straightforward method for predicting the protein structure is to find conformations that have the lowest energy along a chosen folding pathway. One approach in this direction is to produce a large number of structures by varying the dihedral angles of the molecule more or less randomly and then to screen each one using a suitable energy function. This procedure is computationally demanding, but by using a more realistic model, one hopes that the folding behavior one observes in calculations may better mimic the actual folding process in nature. The method is beginning to yield interesting results, thanks to the increase in the computational power but also to the intelligent selection of the folding pathway. This article reviews general features of this method, some important highlights of the particular procedure we used, and some of the more significant results obtained to date in our laboratory. The results are highly encouraging and indicate the direction of future effort that is most likely to be fruitful.