TY - JOUR

T1 - Adjusting potential energy functions for lattice models of chain molecules

AU - Reva, Boris A.

AU - Finkelstein, Alexei V.

AU - Sanner, Michel F.

AU - Olson, Arthur J.

PY - 1996

Y1 - 1996

N2 - 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.

AB - 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.

KW - adjusting of energy functions

KW - lattice approximation error

KW - protein modeling

UR - http://www.scopus.com/inward/record.url?scp=0030017791&partnerID=8YFLogxK

U2 - 10.1002/(SICI)1097-0134(199607)25:3<379::AID-PROT9>3.0.CO;2-A

DO - 10.1002/(SICI)1097-0134(199607)25:3<379::AID-PROT9>3.0.CO;2-A

M3 - Article

C2 - 8844872

AN - SCOPUS:0030017791

SN - 0887-3585

VL - 25

SP - 379

EP - 388

JO - Proteins: Structure, Function and Bioinformatics

JF - Proteins: Structure, Function and Bioinformatics

IS - 3

ER -