Molecular dynamics (MD) simulations play more and more important roles in studying conformations of cyclic peptides in solution. Here we describe how to use replica-exchange molecular dynamics (REMD) implemented in Gromacs software package to simulate peptides with backbone cyclization and stapled peptides with side-chain linkages. Some of our methods for trajectory analyses and our residue-specific force fields are also described.
CITATION STYLE
Jiang, F., & Geng, H. (2019). Computational Methods for Studying Conformational Behaviors of Cyclic Peptides. In Methods in Molecular Biology (Vol. 2001, pp. 61–71). Humana Press Inc. https://doi.org/10.1007/978-1-4939-9504-2_4
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