Biomolecular Simulations: Methods and Protocols

✍ Scribed by Massimiliano Bonomi, Carlo Camilloni

• Publisher: Springer New York;Humana
• Year: 2019
• Tongue: English
• Leaves: 580
• Series: Methods in Molecular Biology 2022
• Edition: 1st ed. 2019
• Category: Library

✦ Synopsis

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.

✦ Table of Contents

Front Matter ....Pages i-xiii
Front Matter ....Pages 1-1
Atomistic Force Fields for Proteins (Robert B. Best)....Pages 3-19
Force Fields for Small Molecules (Fang-Yu Lin, Alexander D. MacKerell Jr)....Pages 21-54
Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field (Ilyas Yildirim)....Pages 55-74
Quantum Chemical and QM/MM Models in Biochemistry (Patricia Saura, Michael Röpke, Ana P. Gamiz-Hernandez, Ville R. I. Kaila)....Pages 75-104
A Practical View of the Martini Force Field (Bart M. H. Bruininks, Paulo C. T. Souza, Siewert J. Marrink)....Pages 105-127
Using SMOG 2 to Simulate Complex Biomolecular Assemblies (Mariana Levi, Prasad Bandarkar, Huan Yang, Ailun Wang, Udayan Mohanty, Jeffrey K. Noel et al.)....Pages 129-151
Front Matter ....Pages 153-153
Replica-Exchange Methods for Biomolecular Simulations (Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, Suyong Re)....Pages 155-177
Metadynamics to Enhance Sampling in Biomolecular Simulations (Jim Pfaendtner)....Pages 179-200
Protein–Ligand Binding Free Energy Calculations with FEP+ (Lingle Wang, Jennifer Chambers, Robert Abel)....Pages 201-232
Ligand-Binding Calculations with Metadynamics (Davide Provasi)....Pages 233-253
The Adaptive Path Collective Variable: A Versatile Biasing Approach to Compute the Average Transition Path and Free Energy of Molecular Transitions (Alberto Pérez de Alba Ortíz, Jocelyne Vreede, Bernd Ensing)....Pages 255-290
Google-Accelerated Biomolecular Simulations (Kai J. Kohlhoff)....Pages 291-309
Front Matter ....Pages 311-311
A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics Using Metainference (Thomas Löhr, Carlo Camilloni, Massimiliano Bonomi, Michele Vendruscolo)....Pages 313-340
Inferring Structural Ensembles of Flexible and Dynamic Macromolecules Using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods (Jürgen Köfinger, Bartosz Różycki, Gerhard Hummer)....Pages 341-352
Modeling Biological Complexes Using Integrative Modeling Platform (Daniel Saltzberg, Charles H. Greenberg, Shruthi Viswanath, Ilan Chemmama, Ben Webb, Riccardo Pellarin et al.)....Pages 353-377
Coevolutionary Analysis of Protein Sequences for Molecular Modeling (Duccio Malinverni, Alessandro Barducci)....Pages 379-397
Coarse Graining of a Giant Molecular System: The Chromatin Fiber (Guido Tiana, Luca Giorgetti)....Pages 399-411
Front Matter ....Pages 413-413
Analyzing Biomolecular Ensembles (Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth et al.)....Pages 415-451
Using Data-Reduction Techniques to Analyze Biomolecular Trajectories (Gareth A. Tribello, Piero Gasparotto)....Pages 453-502
Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis (Toni Giorgino)....Pages 503-527
Analyzing and Biasing Simulations with PLUMED (Giovanni Bussi, Gareth A. Tribello)....Pages 529-578
Back Matter ....Pages 579-581

✦ Subjects

Life Sciences; Bioinformatics; Protein Science; Computer Appl. in Life Sciences