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Abstract Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint.
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Received: 29 April 2015
Revised: 14 June 2015
Accepted manuscript online:
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PACS:
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87.10.-e
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(General theory and mathematical aspects)
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02.50.-r
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(Probability theory, stochastic processes, and statistics)
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| Fund: Project supported in part by the National Natural Science Foundation of China (Grant Nos. 11175224 and 11121403). |
Corresponding Authors:
Zheng Wei-Mou
E-mail: zheng@itp.ac.cn
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Cite this article:
Zheng Wei-Mou (郑伟谋) Knowledge-based potentials in bioinformatics: From a physicist's viewpoint 2015 Chin. Phys. B 24 128701
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