Modeling Side Chains in Peptides and Proteins with the Locally Enhanced Sampling/Simulated Annealing Method

  • Adrian Roitberg
  • Ron Elber


In this chapter, we present the formal basis of a new optimization method that we call LES (locally enhanced sampling) together with applications to side-chain modeling in peptides and proteins. We examine the relationship between an energy function that is derived from data on small model systems and the correct structure of the protein. The question is: Given a functional form for the potential energy of a macromolecule, are the side-chain coordinates at the global energy minimum similar to the x-ray coordinates? This comparison enables us to detect inaccuracies in the force fields that we used (Brooks et al., 1983; Jorgensen and Tirado-Rives, 1988) and possibly to improve them.


Force Field Potential Energy Surface Freezing Temperature Residue Type Minimum Energy Path 
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Copyright information

© Birkhäuser Boston 1994

Authors and Affiliations

  • Adrian Roitberg
  • Ron Elber

There are no affiliations available

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