BIOMOLECULAR SIMULATIONS. METHODS AND PROTOCOLS

1. Atomistic Force Fields for Proteins
2. Force Fields for Small Molecules
3. Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field
4. Quantum Chemical and QM/MM Models in Biochemistry
5. A Practical View of the Martini Force Field
6. Using SMOG 2 to Simulate Complex Biomolecular Assemblies
7. Replica-Exchange Methods for Biomolecular Simulations
8. Metadynamics to Enhance Sampling in Biomolecular Simulations
9. Protein–Ligand Binding Free Energy Calculations with FEP+
10. Ligand-Binding Calculations with Metadynamics
11. The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions
12. Google-Accelerated Biomolecular Simulations
13. A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference
14. Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods
15. Modeling Biological Complexes Using Integrative Modeling Platform
16. Coevolutionary Analysis of Protein Sequences for Molecular Modeling
17. Coarse Graining of a Giant Molecular System: The Chromatin Fiber
18. Analyzing Biomolecular Ensembles
19. Using Data-Reduction Techniques to Analyze Biomolecular Trajectories
20. Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis
21. Analyzing and Biasing Simulations with PLUMED

This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.
Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.

Features
• Includes cutting-edge methods and protocols
• Provides step-by-step detail essential for reproducible results
• Contains key notes and implementation advice from the experts