P. Koehl et M. Delarue, BUILDING PROTEIN LATTICE MODELS USING SELF-CONSISTENT MEAN-FIELD THEORY, The Journal of chemical physics, 108(22), 1998, pp. 9540-9549
An optimization protocol for modeling protein structures on lattice is
proposed which is based on self-consistent mean field (SCMF) theory.
In this procedure, the protein residues are supposed to be independent
, and their possible positions are given by a list of lattice sites. T
o do this, an effective larger system is considered, in which each res
idue i is supposed to occupy all possible sites j, each with a weight
V(i,j) stored in the so-called lattice probability matrix V. The effec
tive energy of the system is computed, and iteratively minimized with
respect to the weights V, the lattice sites being fixed in space. The
final self-consistent V matrix describes the conformational space avai
lable to the protein, based on the energy function implemented. This e
nergy function contains two types of terms, namely simple geometric te
rms which ensure bond connectivity and prevent chain intersection, and
energy terms specific to the problem of interest. The application of
the above protocol to building a lattice model of a protein, given its
three dimensional structure, is discussed and compared with other lat
tice fitting procedures. (C) 1998 American Institute of Physics.