Molecular dynamics simulations: bring biomolecular structures alive on a computer

Shunzhou Wan, Peter V. Coveney, Darren R. Flower

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

Abstract

The molecular dynamics (MD) simulations play a very important role in science today. They have been used successfully in binding free-energy calculations and rational design of drugs and vaccines. MD simulations can help visualize and understand structures and dynamics at an atomistic level when combined with molecular graphics programs. The molecular and atomistic properties can be displayed on a computer in a time-dependent way, which opens a road toward a better understanding of the relationship of structure, dynamics, and function. In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation.
Original languageEnglish
Title of host publicationImmunoinformatics
Subtitle of host publicationpredicting immunogenicity in silico
EditorsDarren R. Flowers
Place of PublicationTotowa, NJ (US)
PublisherHumana Press
Pages321-339
Number of pages19
ISBN (Electronic)978-1-60327-118-9
ISBN (Print)978-1-58829-699-3
DOIs
Publication statusPublished - 16 Jul 2007

Publication series

NameMethods in molecular biology™
PublisherHumana Press
Volume409
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Keywords

  • molecular dynamics simulation
  • visualization
  • major histocompatibility complex

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  • Research Output

    • 5 Chapter (peer-reviewed)
    • 1 Anthology
    • 1 Foreword/postscript

    Immunoinformatics: predicting immunogenicity in silico

    Flower, D. R. (ed.), 16 Jul 2007, Totowa, NJ (US): Humana Press. 438 p. (Methods in molecular biology; vol. 409)

    Research output: Book/ReportAnthology

  • Immunoinformatics and the in silico prediction of immunogenicity: an introduction

    Flower, D. R., 16 Jul 2007, Immunoinformatics: predicting immunogenicity in silico. Flower, D. R. (ed.). Totowa, NJ (US): Humana Press, p. 1-15 15 p. (Methods in molecular biology™; vol. 409).

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

  • In silico prediction of peptide-MHC binding affinity using SVRMHC

    Liu, W., Wan, J., Meng, X., Flower, D. R. & Li, T., 16 Jul 2007, Immunoinformatics: predicting Immunogenicity in silico. Flowers, D. R. (ed.). Totowa, NJ (US): Humana Press, p. 283-291 9 p. (Methods in molecular biology™; vol. 409).

    Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

  • Cite this

    Wan, S., Coveney, P. V., & Flower, D. R. (2007). Molecular dynamics simulations: bring biomolecular structures alive on a computer. In D. R. Flowers (Ed.), Immunoinformatics: predicting immunogenicity in silico (pp. 321-339). (Methods in molecular biology™; Vol. 409). Humana Press. https://doi.org/10.1007/978-1-60327-118-9_24