Bonomi Massimiliano, Camilloni Carlo (eds.) Biomolecular Simulations: Methods and Protocols

Humana Press, 2019. — 580 p. — (Methods in Molecular Biology 2022) — ISBN: 978-1-4939-9607-0This 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.Atomistic and Coarse-Grained Force Fields for Proteins, Small Molecules, and Nucleic Acids
Atomistic Force Fields for Proteins
Force Fields for Small Molecules
Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field
Quantum Chemical and QM/MM Models in Biochemistry
A Practical View of the Martini Force Field
Using SMOG 2 to Simulate Complex Biomolecular Assemblies
Enhanced Sampling and Free-Energy Calculations
Replica-Exchange Methods for Biomolecular Simulations
Metadynamics to Enhance Sampling in Biomolecular Simulations
Protein–Ligand Binding Free Energy Calculations with FEP+
Ligand-Binding Calculations with Metadynamics
The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions
Google-Accelerated Biomolecular Simulations
Integrative Approaches for Biomolecular Simulations
A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference
Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods
Modeling Biological Complexes Using Integrative Modeling Platform
Coevolutionary Analysis of Protein Sequences for Molecular Modeling
Coarse Graining of a Giant Molecular System: The Chromatin Fiber
Analyzing, Visualizing, and Comparing Biomolecular Simulations
Analyzing Biomolecular Ensembles
Using Data-Reduction Techniques to Analyze Biomolecular Trajectories
Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis
Analyzing and Biasing Simulations with PLUMED