Binding free energy of protein/ligand complexes calculated using dissociation Parallel Cascade Selection Molecular Dynamics and Markov state model
Author:
Affiliation:
1. School of Life Science and Technology, Tokyo Institute of Technology
2. Physics Department, Faculty of Science, Ain Shams University
Publisher
Biophysical Society of Japan
Subject
General Medicine
Link
https://www.jstage.jst.go.jp/article/biophysico/18/0/18_bppb-v18.037/_pdf
Reference68 articles.
1. [1] Lelièvre, T., Rousset, M., Stoltz, G. Free energy computations: A mathematical perspective (Imperial College Press, London, 2010). https://doi.org/10.1142/p579
2. [2] Plattner, N., Noé, F. Protein conformational plasticity and complex ligand-binding kinetics explored by atomistic simulations and Markov models. Nat. Commun. 6, 7653 (2015). https://doi.org/10.1038/ncomms8653
3. [3] Tiana, G., Simona, F., De Mori, G. M. S., Broglia, R. A., Colombo, G. Understanding the determinants of stability and folding of small globular proteins from their energetics. Protein Sci. 13, 113–124 (2004). https://doi.org/10.1110/ps.03223804
4. [4] Wang, W., Donini, O., Reyes, C. M., Kollman, P. A. Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, Protein-Ligand, Protein-Protein, and Protein-Nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomol. Struct. 30, 211–243 (2001). https://doi.org/10.1146/annurev.biophys.30.1.211
5. [5] Brooijmans, N., Kuntz, I. D. Molecular recognition and docking algorithms. Annu. Rev. Biophys. Biomol. Struct. 32, 335–373 (2003). https://doi.org/10.1146/annurev.biophys.32.110601.142532
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