Biomolecular Simulations

Methods and Protocols

Massimiliano Bonomi, Carlo Camilloni (Herausgeber)

Buch | Hardcover

581 Seiten

2019 | 1st ed. 2019
Humana Press Inc. (Verlag)
978-1-4939-9607-0 (ISBN)

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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.

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.- Replica Exchange Methods for Biomolecular Simulations.- Metadynamics to Enhance Sampling in Biomolecular Simulations.- Protein-Ligand Binding Free Energy Calculations with FEP+.- Ligand Binging 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.- 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.- Co-Evolutionary Analysis of Protein Sequences for Molecular Modeling.- Coarse Graining of a Giant Molecular System: The Chromatin Fiber.- 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.

Erscheinungsdatum	23.08.2019
Reihe/Serie	Methods in Molecular Biology ; 2022
Zusatzinfo	155 Illustrations, color; 30 Illustrations, black and white; XIII, 581 p. 185 illus., 155 illus. in color.
Verlagsort	Totowa, NJ
Sprache	englisch
Maße	178 x 254 mm
Themenwelt	Mathematik / Informatik ► Informatik ► Theorie / Studium
	Informatik ► Weitere Themen ► Bioinformatik
	Naturwissenschaften ► Biologie ► Biochemie
	Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
Schlagworte	Bioinformatics • Force Fields • kinetics calculations • Ligand binding • maximum entropy
ISBN-10	1-4939-9607-X / 149399607X
ISBN-13	978-1-4939-9607-0 / 9781493996070
Zustand	Neuware