Skip to main content
Springer Nature Link
Log in

Biomolecular Simulations

Methods and Protocols

  • Book
  • © 2013

Overview

Editors:
  1. Luca Monticelli

    1. DSIMB, UMR-S 665, INSERM, Paris, France

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  2. Emppu Salonen

    1. , Department of Applied Physics, Aalto University, AALTO, Finland

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

  • Illustrates methods commonly used in molecular modeling of biological systesms
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts
  • Includes supplementary material: sn.pub/extras

Part of the book series: Methods in Molecular Biology (MIMB, volume 924)

This is a preview of subscription content, log in via an institution to check access.

Access this book

Log in via an institution
eBook USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Other ways to access

Licence this eBook for your library

Institutional subscriptions

About this book

Over the past 40 years the field of molecular simulations has evolved from picosecond studies of isolated macromolecules in vacuum to studies of complex, chemically heterogeneous biological systems consisting of millions of atoms, with the simulation time scales spanning up to milliseconds. In Biomolecular Simulations: Methods and Protocols, expert researchers illustrate many of the methods commonly used in molecular modelling of biological systems, including methods for electronic structure calculations, classical molecular dynamics simulations and coarse-grained techniques. A selection of advanced techniques and recent methodological developments, which rarely find coverage in traditional textbooks, is also introduced.

 

Written in the highly successful Methods in Molecular Biology series format, chapters include general introductions to well-established computational methodologies, applications to real-world biological systems, as well as practical tips and general protocols on carrying out biomolecular simulations. Special emphasis is placed on simulations of proteins, lipids, nucleic acids, and carbohydrates. Authoritative and practical, Biomolecular Simulations: Methods and Protocols seeks to aid scientists in further simulation studies of biological systems.

Similar content being viewed by others

Keywords

Table of contents (26 protocols)

  1. Front Matter

    Pages i-xiii
    Download chapter PDF

  2. Quantum Mechanics Calculations

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Ab Initio, Density Functional Theory, and Semi-Empirical Calculations

      • Mikael P. Johansson, Ville R. I. Kaila, Dage Sundholm
      Pages 3-27

    3. Ab Initio Molecular Dynamics

      • Kari Laasonen
      Pages 29-42

    4. Introduction to QM/MM Simulations

      • Gerrit Groenhof
      Pages 43-66

    5. Computational Enzymology

      • Alessio Lodola, Adrian J. Mulholland
      Pages 67-89

    6. QM and QM/MM Simulations of Proteins

      • Thomas Steinbrecher, Marcus Elstner
      Pages 91-124

  3. Classical Mechanics: Atomistic Simulations

    1. Front Matter

      Pages 125-125
      Download chapter PDF

    2. Classical Molecular Dynamics in a Nutshell

      • Susanna Hug
      Pages 127-152

    3. Enhanced Sampling Algorithms

      • Ayori Mitsutake, Yoshiharu Mori, Yuko Okamoto
      Pages 153-195

    4. Force Fields for Classical Molecular Dynamics

      • Luca Monticelli, D. Peter Tieleman
      Pages 197-213

    5. Polarizable Force Fields

      • Hanne S. Antila, Emppu Salonen
      Pages 215-241

    6. Electrostatics Interactions in Classical Simulations

      • G. Andrés Cisneros, Volodymyr Babin, Celeste Sagui
      Pages 243-270

    7. An Introduction to Best Practices in Free Energy Calculations

      • Michael R. Shirts, David L. Mobley
      Pages 271-311

    8. Recipes for Free Energy Calculations in Biomolecular Systems

      • Mahmoud Moradi, Volodymyr Babin, Celeste Sagui, Christopher Roland
      Pages 313-337

    9. Molecular Docking Methodologies

      • Andrea Bortolato, Marco Fanton, Jonathan S. Mason, Stefano Moro
      Pages 339-360

    10. Simulation Studies of the Mechanism of Membrane Transporters

      • Giray Enkavi, Jing Li, Paween Mahinthichaichan, Po-Chao Wen, Zhijian Huang, Saher A. Shaikh et al.
      Pages 361-405

    11. Molecular Dynamics Simulations of Lipid Bilayers: Simple Recipe of How to Do It

      • Hector Martinez-Seara, Tomasz Róg
      Pages 407-429

    12. Simulations of Lipid Monolayers

      • Svetlana Baoukina, D. Peter Tieleman
      Pages 431-444

    13. Simulating DNA by Molecular Dynamics: Aims, Methods, and Validation

      • Nicolas Foloppe, Marc Guéroult, Brigitte Hartmann
      Pages 445-468
Back to top

Editors and Affiliations

  • DSIMB, UMR-S 665, INSERM, Paris, France

    Luca Monticelli

  • , Department of Applied Physics, Aalto University, AALTO, Finland

    Emppu Salonen

Bibliographic Information

  • Book Title: Biomolecular Simulations

  • Book Subtitle: Methods and Protocols

  • Editors: Luca Monticelli, Emppu Salonen

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-62703-017-5

  • Publisher: Humana Totowa, NJ

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2013

  • Hardcover ISBN: 978-1-62703-016-8Published: 04 October 2012

  • Softcover ISBN: 978-1-4939-5891-7Published: 23 August 2016

  • eBook ISBN: 978-1-62703-017-5Published: 04 October 2012

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XIII, 702

  • Topics: Bioinformatics, Computer Appl. in Life Sciences

Publish with us

Policies and ethics

Back to top