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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
What is a desirable statistical energy function for proteins and how can it be obtained?
Yaoqi Zhou1, Hongyi Zhou, Chi Zhang
1Howard Hughes Medical Institute Center for Single Molecule Biophysics, Department of Physiology and Biophysics, State University of New York at Buffalo, 124 Sherman Hall, Buffalo, NY 14214, USA. yqzhou@buffalo.edu
Cell Biochemistry and Biophysics
|October 3, 2006
Summary
Researchers developed a statistical energy function for proteins using a physical reference state. This approach aims for accuracy and transferability, overcoming limitations of purely statistical methods in protein structure analysis.
Area of Science:
- Structural biology
- Computational biophysics
- Bioinformatics
Background:
- Statistical analysis of protein structures often yields energy functions lacking physical realism.
- Existing methods may require numerous adjustable parameters and exhibit limited transferability.
Purpose of the Study:
- To investigate the feasibility of deriving a physically meaningful energy function from statistical data.
- To develop a statistical energy function with desirable properties of physical models.
Main Methods:
- Introduction of a simple physical-based reference state: DFIRE (Distance-scaled, Finite, Ideal-gas REference state).
- Statistical analysis of protein structures informed by the DFIRE reference state.
Main Results:
- Demonstration that a desirable, physically-founded statistical energy function can be obtained.
- The DFIRE approach provides a basis for energy functions that are database independent and transferable.
Conclusions:
- A statistical energy function with desirable physical characteristics is achievable.
- DFIRE offers a promising route towards accurate and broadly applicable protein energy functions.
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