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Biophys J. 2005 Nov;89(5):3008-16.

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

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  • 1Graduate Group in Biophysics, and Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA 94143, USA.


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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