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An Information Theoretic Approach to Macromolecular Modeling: II. Force Fields

Tiba Aynechi ^* and Irwin D. Kuntz 

^* Graduate Group in Biophysics, and Department of Pharmaceutical Chemistry, University of California, San Francisco, California

Correspondence: Address reprint requests to Dr. Irwin D. Kuntz, Dept. of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, CA 94143-0446. Tel.: 415-476-1937; Fax: 415-502-1411; E-mail: kuntz{at}cgl.ucsf.edu.

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.

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				T. Aynechi and I. D. Kuntz An Information Theoretic Approach to Macromolecular Modeling: I. Sequence Alignments Biophys. J., November 1, 2005; 89(5): 2998 - 3007. [Abstract] [Full Text] [PDF]