Adjusting potential energy functions for lattice models of chain molecules.
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.
Reva
B A
BA
Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037, USA.
Finkelstein
A V
AV
Sanner
M F
MF
Olson
A J
AJ
D008956:Models, Chemical; D011506:Proteins / Q000737:chemistry*
D011506:Proteins