Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
نویسندگان
چکیده
منابع مشابه
Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
A Monte Carlo-minimization method has been developed to overcome the multiple-minima problem. The Metropolis Monte Carlo sampling, assisted by energy minimization, surmounts intervening barriers in moving through successive discrete local minima in the multidimensional energy surface. The method has located the lowest-energy minimum thus far reported for the brain pentapeptide [Met5]enkephalin ...
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Protein folding is a very difficult global optimization problem. Furthermore it is coupled with the difficult task of designing a reliable force field with which one has to search for the global minimum. A summary of a series of optimization methods developed and applied to various problems involving polypeptide chains is described in this paper. With recent developments, a computational treatm...
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We demonstrate that evolutionary Monte Carlo ~EMC! can be applied successfully to simulations of protein folding on simple lattice models, and to finding the ground state of a protein. In all cases, EMC is faster than the genetic algorithm and the conventional Metropolis Monte Carlo, and in several cases it finds new lower energy states. We also propose one method for the use of secondary struc...
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c © 2003 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher ment...
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We demonstrate that the recently proposed pruned-enriched Rosenbluth method (PERM) (Grassberger, Phys. Rev. E 56:3682, 1997) leads to extremely efficient algorithms for the folding of simple model proteins. We test it on several models for lattice heteropolymers, and compare it to published Monte Carlo studies of the properties of particular sequences. In all cases our method is faster than the...
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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 1987
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.84.19.6611