Biomolecular Simulations

Methods and Protocols

  • Massimiliano Bonomi
  • Carlo Camilloni

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

Table of contents

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

    1. Front Matter
      Pages 1-1
    2. Robert B. Best
      Pages 3-19
    3. Fang-Yu Lin, Alexander D. MacKerell Jr
      Pages 21-54
    4. Patricia Saura, Michael Röpke, Ana P. Gamiz-Hernandez, Ville R. I. Kaila
      Pages 75-104
    5. Bart M. H. Bruininks, Paulo C. T. Souza, Siewert J. Marrink
      Pages 105-127
    6. 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
    2. Yuji Sugita, Motoshi Kamiya, Hiraku Oshima, Suyong Re
      Pages 155-177
    3. Lingle Wang, Jennifer Chambers, Robert Abel
      Pages 201-232
    4. Davide Provasi
      Pages 233-253
    5. Kai J. Kohlhoff
      Pages 291-309
  4. Integrative Approaches for Biomolecular Simulations

    1. Front Matter
      Pages 311-311
    2. Thomas Löhr, Carlo Camilloni, Massimiliano Bonomi, Michele Vendruscolo
      Pages 313-340
    3. Daniel Saltzberg, Charles H. Greenberg, Shruthi Viswanath, Ilan Chemmama, Ben Webb, Riccardo Pellarin et al.
      Pages 353-377
    4. Duccio Malinverni, Alessandro Barducci
      Pages 379-397
    5. Guido Tiana, Luca Giorgetti
      Pages 399-411
  5. Analyzing, Visualizing, and Comparing Biomolecular Simulations

    1. Front Matter
      Pages 413-413
    2. Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth et al.
      Pages 415-451
    3. Gareth A. Tribello, Piero Gasparotto
      Pages 453-502
    4. Giovanni Bussi, Gareth A. Tribello
      Pages 529-578
  6. Back Matter
    Pages 579-581

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.


bioinformatics force fields kinetics calculations ligand binding maximum Entropy

Editors and affiliations

  • Massimiliano Bonomi
    • 1
  • Carlo Camilloni
    • 2
  1. 1.Structural Bioinformatics UnitInstitut Pasteur, CNRS UMR 3528ParisFrance
  2. 2.Dipartimento di BioscienzeUniversità degli Studi di MilanoMilanoItaly

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC, part of Springer Nature 2019
  • Publisher Name Humana, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-9607-0
  • Online ISBN 978-1-4939-9608-7
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site