An information theoretic approach to macromolecular modeling: II. Force fields

Abstract

In this article, we explore the information content of molecular force-field calculations. We make use of exhaustive lattice models of molecular conformations and reduced alphabet sequences to determine the relative resolving power of pairwise interaction-based force fields. We find that sequence-specific interactions that operate over longer distances offer greater amounts of information than nearest-neighbor or non-sequence-specific interactions. In a companion article in this issue, we explored the information content of sequence alignment procedures and the calculation of gap penalties. Both articles have implications for protein and nucleic-acid computations. © 2005 by the Biophysical Society.