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Biomolecular Simulations

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Massimiliano Bonomi

    1. Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

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  2. Carlo Camilloni

    1. Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

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    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2022)

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About this book

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.


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Table of contents (21 protocols)

  1. Front Matter

    Pages i-xiii
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  2. Atomistic and Coarse-Grained Force Fields for Proteins, Small Molecules, and Nucleic Acids

    1. Front Matter

      Pages 1-1
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    2. Atomistic Force Fields for Proteins

      • Robert B. Best
      Pages 3-19

    3. Force Fields for Small Molecules

      • Fang-Yu Lin, Alexander D. MacKerell Jr
      Pages 21-54

    4. Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field

      • Ilyas Yildirim
      Pages 55-74

    5. Quantum Chemical and QM/MM Models in Biochemistry

      • Patricia Saura, Michael Röpke, Ana P. Gamiz-Hernandez, Ville R. I. Kaila
      Pages 75-104

    6. A Practical View of the Martini Force Field

      • Bart M. H. Bruininks, Paulo C. T. Souza, Siewert J. Marrink
      Pages 105-127

    7. 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

  3. Enhanced Sampling and Free-Energy Calculations

    1. Front Matter

      Pages 153-153
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    2. Replica-Exchange Methods for Biomolecular Simulations

      • Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, Suyong Re
      Pages 155-177

    3. Metadynamics to Enhance Sampling in Biomolecular Simulations

      • Jim Pfaendtner
      Pages 179-200

    4. Protein–Ligand Binding Free Energy Calculations with FEP+

      • Lingle Wang, Jennifer Chambers, Robert Abel
      Pages 201-232

    5. Ligand-Binding Calculations with Metadynamics

      • Davide Provasi
      Pages 233-253

    6. 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

    7. Google-Accelerated Biomolecular Simulations

      • Kai J. Kohlhoff
      Pages 291-309

  4. Integrative Approaches for Biomolecular Simulations

    1. Front Matter

      Pages 311-311
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    2. 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

    3. 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

    4. 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

    5. Coevolutionary Analysis of Protein Sequences for Molecular Modeling

      • Duccio Malinverni, Alessandro Barducci
      Pages 379-397
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Editors and Affiliations

  • Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

    Massimiliano Bonomi

  • Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

    Carlo Camilloni

Bibliographic Information

  • Book Title: Biomolecular Simulations

  • Book Subtitle: Methods and Protocols

  • Editors: Massimiliano Bonomi, Carlo Camilloni

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9608-7

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9607-0Published: 08 August 2019

  • Softcover ISBN: 978-1-4939-9610-0Published: 14 August 2020

  • eBook ISBN: 978-1-4939-9608-7Published: 08 August 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 581

  • Number of Illustrations: 30 b/w illustrations, 155 illustrations in colour

  • Topics: Bioinformatics, Protein Science, Computer Appl. in Life Sciences

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