Journal
CELL BIOCHEMISTRY AND BIOPHYSICS
Volume 46, Issue 2, Pages 165-174Publisher
HUMANA PRESS INC
DOI: 10.1385/CBB:46:2:165
Keywords
knowledge-based potential; hydrophobicity; protein-ligand binding affinity; database dependence
Funding
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM068530] Funding Source: NIH RePORTER
- NIGMS NIH HHS [R01 GM 068530, R01 GM 966049] Funding Source: Medline
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Can one obtain a physical energy function for proteins from statistical analysis of protein structures? A direct answer to this question is likely no. A less demanding question is whether one can produce a statistical energy function that has the desirable features of a physical-based energy function. Such a desirable energy function would be founded on a physical basis with few or no adjustable parameters, reproduce the known physical characters of amino acid residues, be mostly database independent and transferable, and, more importantly, reasonably accurate in various applications. In this review, we show how such a desirable energy function can be obtained via introducing a simple physical-based reference state called DFIRE (Distance-scaled, Finite, Ideal-gas REference state).
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