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Adjusting potential energy functions for lattice models of chain molecules

✍ Scribed by Reva, Boris A.; Finkelstein, Alexei V.; Sanner, Michel F.; Olson, Arthur J.

Publisher
John Wiley and Sons
Year
1996
Tongue
English
Weight
696 KB
Volume
25
Category
Article
ISSN
0887-3585

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✦ Synopsis

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 22:10&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. 981-14, 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. o 1996

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