On statistical energy functions for biomolecular modeling and design

Abstract

Statistical energy functions are general models about atomic or residue-level interactions in biomolecules, derived from existing experimental data. They provide quantitative foundations for structural modeling as well as for structure-based protein sequence design. Statistical energy functions can be derived computationally either based on statistical distributions or based on variational assumptions. We present overviews on the theoretical assumptions underlying the various types of approaches. Theoretical considerations underlying important pragmatic choices are discussed.

Graphical abstract

Keywords

potential of mean forces / statistical distribution / optimization / correlated variable / reference state

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ACKNOWLEDGEMENTS

This work has been supported by National Natural Science Foundation of China (Grant Nos 31370755 and 21173203) and the Chinese Ministry of Science and Technology (Grant No. 2012AA02A704).

COMPLIANCE WITH ETHICS GUIDELINES

The author Haiyan Liu declare that he has no conflict of interests.

This article does not contain any studies with human or animal subjects performed by the author.

RIGHTS & PERMISSIONS

2015 Higher Education Press and Springer-Verlag Berlin Heidelberg