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Molecular Modeling of Peptides

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Computational Peptidology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1268))

Abstract

This article presents a review of the field of molecular modeling of peptides. The main focus is on atomistic modeling with molecular mechanics potentials. The description of peptide conformations and solvation through potentials is discussed. Several important computer simulation methods are briefly introduced, including molecular dynamics, accelerated sampling approaches such as replica-exchange and metadynamics, free energy simulations and kinetic network models like Milestoning. Examples of recent applications for predictions of structure, kinetics, and interactions of peptides with complex environments are described. The reliability of current simulation methods is analyzed by comparison of computational predictions obtained using different models with each other and with experimental data. A brief discussion of coarse-grained modeling and future directions is also presented.

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Acknowledgements

The figures were prepared using MolScript [146, 147], Raster3D [148], ImageMagick [149], and Grace [150].

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  1. Departments of Chemistry and Molecular Biosciences, University of Kansas, 1251 Wescoe Hall Drive, Room 5090, Lawrence, KS, 66045, USA

    Krzysztof Kuczera

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  1. Krzysztof Kuczera
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  1. Center of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China

    Peng Zhou

  2. Center of Bioinformatics (COBI), School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China

    Jian Huang

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Kuczera, K. (2015). Molecular Modeling of Peptides. In: Zhou, P., Huang, J. (eds) Computational Peptidology. Methods in Molecular Biology, vol 1268. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2285-7_2

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  • DOI: https://doi.org/10.1007/978-1-4939-2285-7_2

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