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Statistical Contact Potentials in Protein Coarse-Grained Modeling: From Pair to Multi-body Potentials

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Multiscale Approaches to Protein Modeling

Abstract

The basic concepts of coarse-graining protein structures led to the introduction of empirical statistical potentials in protein computations. We review the history of the development of statistical contact potentials in computational biology and discuss the common features and differences between various pair contact potentials. Potentials derived from the statistics of non-bonded contacts in protein structures from the Protein Data Bank (PDB) are compared with potentials developed for threading purposes based on the optimization of the selection of the native structures among decoys. The energy of transfer of amino acids from water to a protein environment is discussed in detail. We suggest that a next generation of statistical contact potentials should include the effects of residue packing in proteins to improve predictions of protein native three-dimensional structures. We review existing multi-body potentials that have been proposed in the literature, including our own recent four-body potentials. We show how these are related to amino acid substitution matrices.

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Acknowledgments

We acknowledge the financial support provided by NIH grants 1R01GM073095-3, 1R01GM072014-5, and 1R01GM081680-2.

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Authors and Affiliations

  1. Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, USA

    Sumudu P. Leelananda, Yaping Feng, Andrzej Kloczkowski & Robert L. Jernigan

  2. L.H.Baker Center for Bioinformatics and Biological Statistics, Iowa State University, Ames, IA, USA

    Sumudu P. Leelananda, Yaping Feng, Pawel Gniewek, Andrzej Kloczkowski & Robert L. Jernigan

  3. Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Warsaw, Poland

    Pawel Gniewek

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  1. Sumudu P. Leelananda
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  2. Yaping Feng
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Correspondence to Robert L. Jernigan .

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  1. Dept. Chemistry, University of Warsaw, ul. Pasteura 1, Warszawa, 02-093, Poland

    Andrzej Kolinski

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Leelananda, S.P., Feng, Y., Gniewek, P., Kloczkowski, A., Jernigan, R.L. (2011). Statistical Contact Potentials in Protein Coarse-Grained Modeling: From Pair to Multi-body Potentials. In: Kolinski, A. (eds) Multiscale Approaches to Protein Modeling. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-6889-0_6

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