Adjusting potential energy functions for lattice models of chain molecules

Boris A. Reva, Alexei V. Finkelstein, Michel F. Sanner, Arthur J. Olson

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11 Scopus citations


Lattice models of proteins can approximate off-lattice structures 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 Å). 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 Å, the lattice-adjusted potentials improve the accuracy of lattice-based energy calculations and increase the correlations between off-lattice and lattice energies.

Original languageEnglish
Pages (from-to)379-388
Number of pages10
JournalProteins: Structure, Function and Bioinformatics
Issue number3
StatePublished - 1996
Externally publishedYes


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


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