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Adjusting potential energy functions for lattice models of chain molecules

Academic Article
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Overview

authors

  • Reva, B. A.
  • Finkelstein, A. V.
  • Sanner, Michel
  • Olson, Arthur

publication date

  • July 1996

journal

  • Proteins-Structure Function and Genetics  Journal

abstract

  • Lattice models of proteins can approximate off-lattice structure to arbitrary precision with RMS (root mean squared) deviations roughly equal to half the lattice spacing (Rykunov et al., Proteins 22:100-109, 1995; Reva et al., J. Comp. Biol., 1996). However, even small distortions in the positions of chain links lead to significant errors in lattice-based energy calculations (Reva et al., J. Comp. Chem., 1996). These errors arise mainly from rigid interactions (such as steric repulsion) which change their energies considerably at a range which is much smaller than the usual accuracy of lattice modeling (> 1.0 A). To reduce this error, we suggest a procedure of adjusting energy functions to a given lattice. The general approach is illustrated with energy calculations based on pairwise potentials by Kolinski et al. (J. Chem. Phys. 98:1-14, 1993). At all the lattice spacings, from 0.5-3.8 A, the lattice-adjusted potentials improve the accuracy of lattice-based energy calculations and increase the correlations between off-lattice and lattice energies.

subject areas

  • Models, Chemical
  • Proteins
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Research

keywords

  • adjusting of energy functions
  • lattice approximation error
  • protein modeling
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Identity

International Standard Serial Number (ISSN)

  • 0887-3585

Digital Object Identifier (DOI)

  • 10.1002/(sici)1097-0134(199607)25:3<379::aid-prot9>3.0.co;2-a

PubMed ID

  • 8844872
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Additional Document Info

start page

  • 379

end page

  • 388

volume

  • 25

issue

  • 3

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