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Cell Biochemistry and Biophysics

, Volume 46, Issue 2, pp 165–174 | Cite as

What is a desirable statistical energy functions for proteins and how can it be obtained?

  • Yaoqi Zhou
  • Hongyi Zhou
  • Chi Zhang
  • Song Liu
Review

Abstract

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 DRIRE (Distance-scaled, Finite, Ideal-gas Reference state).

Index Entries

knowledge-based potential hydrophobicity protein-ligand binding affinity database dependence 

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Copyright information

© Humana Press Inc. 2006

Authors and Affiliations

  1. 1.Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and BiophysicsState University of New York at BuffaloBuffalo

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