Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules, A
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| Summary: | online resource (244 pages) text |
| Language: | English |
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Melville, New York
AIP Publishing
2023
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| Online Access: | https://doi.org/10.1063/9780735425279 |
| Format: | Electronic Book |
Table of Contents:
- A Practical Introduction to Martini 3 and Its Application to Protein-Ligand Binding Simulations — Multiscale Theoretical Studies for Molecular Motors — Simulating Transmembrane Proteins with the Coarse-Grained SIRAH Force Field: Tips and Tricks for Setting Up and Running in AMBER — A Guide to Titratable Martini Simulations — Simulating Membrane Proteins with Constant pH Molecular Dynamics — Learning DeePMD-kit: A Guide to Building Deep Potential Models — Enhanced Sampling Based on Collective Variables — A Practical Guide to Kinetics Calculation of Protein Conformational Change Using Frequency Adaptive Metadynamics — TAPS: A Traveling-Salesman Based Automated Path Searching Method for Functional Dynamics of Complex Biomolecular Systems — A Step-by-Step Guide on How to Construct Quasi-Markov State Models to Study Functional Conformational Changes of Biological Macromolecules — Calculation of Relative Binding Free Energy for Mutations in Protein Complexes: The Alchemical Path — Appendix — Index.