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Conformation Searching Using Simulated Annealing

  • Stephen R. Wilson
  • Weili Cui

Abstract

Protein folding by direct computer-directed conformation searching is not yet possible (Brunger and Karplus, 1991). Two fundamental problems challenge researchers in this area. The first involves the general issue of energy calculations for large molecules, i.e., parameters, solvents, etc. The second is a more fundamental one called the multiple minimum problem. Since the number of possible minima is an exponential function of the number of degrees of freedom (rotatable angles), an a priori search for the lowest-energy solution to such a problem is impossible for more than about 15 rotatable angles, even with today’s fastest computers. A classic example of this type of problem is known as the “Traveling Salesman Problem” (Kalos and Whitlock, 1986). The problem goes as follows: Try to find the shortest route (i.e., cheapest airfare) for a hypothetical salesman as he/she visits an increasing number of cities.

Keywords

Simulated Annealing Global Minimum Metropolis Algorithm Conformational Search Amber Force Field 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Birkhäuser Boston 1994

Authors and Affiliations

  • Stephen R. Wilson
  • Weili Cui

There are no affiliations available

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