An information theoretic approach to macromolecular modeling: II. Force fields.
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.
Aynechi
Tiba
T
Graduate Group in Biophysics, and Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA 94143, USA.
Kuntz
Irwin D
ID
D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D019277:Entropy; D019143:Evolution, Molecular; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry; D016415:Sequence Alignment; D012984:Software; D055672:Static Electricity; D013696:Temperature; D013816:Thermodynamics
D011506:Proteins