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Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes pp 89–115Cite as

Physics-Based Modeling of Side Chain—Side Chain Interactions in the UNRES Force Field

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Part of the book series: Springer Series on Bio- and Neurosystems ((SSBN,volume 8))

Abstract

Work on a development of a new model of side-chain—side-chain interactions for side-chains of amino acids, to be used in the UNRES force-field and in other large-scale simulations, has been described in this chapter. In the presented model a polar/charged side chain consists of two sites of interaction, nonpolar and polar. General expressions for the effective energy of interaction between amino acids are given depending on the kind of interacting pair. Results of tests with the new UNRES force-field parameters have also been shown together with an extension of the force-field for the phosphorylated amino-acids in this chapter. The results of the studies on the influence of particle size on the free-energy profile of hydrophobic interactions, and the temperature dependence of the potential of mean force for side chain—side chain interactions are also presented.

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Acknowledgements

This research was conducted by using the resources of (a) our 818-processor Beowulf cluster at the Baker Laboratory of Chemistry and Chemical Biology, Cornell University, (b) the National Science Foundation Terascale Computing System at the Pittsburgh Supercomputer Center, (c) 45-processor Beowulf cluster at the Faculty of Chemistry, University of Gdańsk, (d) the Informatics Center of the Metropolitan Academic Network (IC MAN) in Gdańsk. This work was supported by grants from the U.S. National Institutes of Health (GM-14312), the U.S. National Science Foundation (MCB05-41633), the Polish Ministry of Science and Education (N N204 152836), and the Polish National Science Centre (UMO-2013/10/E/ST4/00755).

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  1. Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland

    Mariusz Makowski

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  1. Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland

    Adam Liwo

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Makowski, M. (2019). Physics-Based Modeling of Side Chain—Side Chain Interactions in the UNRES Force Field. In: Liwo, A. (eds) Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Series on Bio- and Neurosystems, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-95843-9_4

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