Monte Carlo-minimization approach to the multiple-minima problem in protein folding.
Zhenqin Li,Harold A. Scheraga +1 more
TLDR
The Monte Carlo-minimization method has located the lowest-energy minimum thus far reported for the brain pentapeptide [Met5]enkephalin in the absence of water, presumably it is the global minimum-energy structure.Abstract:
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 in the absence of water. Presumably it is the global minimum-energy structure. This supports the concept that protein folding may be a Markov process. In the presence of water, the molecules appear to exist as an ensemble of different conformations.read more
Citations
More filters
Journal ArticleDOI
CHARMM: the biomolecular simulation program.
Bernard R. Brooks,Charles L. Brooks,Alexander D. MacKerell,Lennart Nilsson,Robert J. Petrella,Benoît Roux,Youngdo Won,Georgios Archontis,Christian Bartels,Stefan Boresch,Amedeo Caflisch,Leo S. D. Caves,Qiang Cui,Aaron R. Dinner,Michael Feig,Stefan Fischer,Jiali Gao,Milan Hodošček,Wonpil Im,K. Kuczera,Themis Lazaridis,Jianpeng Ma,V. Ovchinnikov,Emanuele Paci,Richard W. Pastor,Carol Beth Post,Jingzhi Pu,M. Schaefer,Bruce Tidor,Richard M. Venable,H. L. Woodcock,Xiongwu Wu,Wei Yang,Darrin M. York,Martin Karplus,Martin Karplus +35 more
TL;DR: An overview of the CHARMM program as it exists today is provided with an emphasis on developments since the publication of the original CHARMM article in 1983.
Journal ArticleDOI
Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms
TL;DR: In this paper, the potential energy surface is transformed into a collection of interpenetrating staircases, and the lowest known structures are located for all Lennard-Jones clusters up to 110 atoms, including a number that have never been found before in unbiased searches.
Book ChapterDOI
Protein Structure Prediction Using Rosetta
TL;DR: This chapter elaborates protein structure prediction using Rosetta, where short fragments of known proteins are assembled by a Monte Carlo strategy to yield native-like protein conformations.
Journal ArticleDOI
ICM—a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation
TL;DR: It is concluded that the most promising detailed approach to the protein‐folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space.
Journal ArticleDOI
Structural properties of nanoclusters: Energetic, thermodynamic, and kinetic effects
TL;DR: In this paper, a review of the experimental methods for the production of free nanoclusters is presented, along with theoretical and simulation issues, always discussed in close connection with the experimental results.
References
More filters
Frontiers in chemistry
TL;DR: Progress in chemical synthesis depends on comparable advances in other branches of chemistry, such as in analysis, methods for determining the intimate details of chemical structures and of reaction mechanisms, and theories of chemical structure and reactions.