Improvement of the relative entropy based protein folding method

The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble average of the contact potential was estimated by an approximate calculation. In...

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Bibliographic Details
Published in:Science China. Physics, mechanics & astronomy mechanics & astronomy, 2009-06, Vol.52 (6), p.885-892
Main Authors: Qi, LiSheng, Su, JiGuo, Chen, WeiZu, Wang, CunXin
Format: Article
Language:English
Subjects:
Algorithms
Astronomy
Classical and Continuum Physics
Contact potentials
Entropy
folding
Mathematical analysis
method
minimization
Observations and Techniques
perturbation
Perturbation theory
Physics
Physics and Astronomy
protein
Proteins
relative
thermodynamic
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Summary:The "relative entropy" has been used as a minimization function to predict the tertiary structure of a protein backbone, and good results have been obtained. However, in our previous work, the ensemble average of the contact potential was estimated by an approximate calculation. In order to improve the theoretical integrity of the relative-entropy-based method, a new theoretical calculation method of the ensemble average of the contact potential was presented in this work, which is based on the thermodynamic perturbation theory. Tests of the improved algorithm were performed on twelve small proteins. The root mean square deviations of the predicted versus the native structures from Protein Data Bank range from 0.40 to 0.60 nm. Compared with the previous approximate values, the average prediction accuracy is improved by 0.04 nm.
ISSN:1674-7348
1672-1799
1869-1927
1862-2844
DOI:10.1007/s11433-009-0112-3