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Author: Kolinski, Andrzej × Author: Skolnick, Jeffrey × Author: Vieth, Michal × Item Type: Publication × Has files: Yes ×

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A hierarchical approach to the prediction of the quaternary structure of GCN4 and its mutants

1996 , Vieth, Michal , Kolinski, Andrzej , Brooks, C. L., III , Skolnick, Jeffrey

A hierarchical approach to protein folding is employed to examine the folding pathway and predict the quaternary structure of the GCN4 leucine zipper. Structures comparable in quality to experiment have been predicted. In addition, the equilibrium between dimers, trimers and tetramers of a number of GCN4 mutants has been examined. In five out of eight cases, the simulation results are in accordance with the experimental studies of Harbury, et al.

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A simple technique to estimate partition functions and equilibrium constants from Monte Carlo simulations

1995-04-15 , Vieth, Michal , Kolinski, Andrzej , Skolnick, Jeffrey

A combined Monte Carlo (MC) simulation-statistical mechanical treatment is proposed to calculate the internal partition function and equilibrium constant. The method has been applied to a number of one and multidimensional analytical functions. When sampling is incomplete, various factorization approximations for estimating the partition function are discussed. The resulting errors are smaller when the ratios of the partition functions are calculated (as in the determination of equilibrium constants) as opposed to the partition function itself.

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