Israel Journal of Chemistry
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Significance of Molecular Dynamics Simulations for Life Sciences

Authors

  • Martin Karplus,

    Corresponding author
    1. Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138 (USA)
    2. L'Institut de Science et d'Ingénierie Supramoléculaires (ISIS), Université Louis Pasteur, 8 allée Gaspard Monge, 67000 Strasbourg (France)

    • Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138 (USA)===

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  • Richard Lavery

    1. Bases Moléculaires et Structurales des Systèmes Infectieux, CNRS UMR 5086/Univ. Lyon I, IBCP, 7 passage du Vercors, Lyon 69367 (France)
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Abstract

This article illustrates by examples the limited acceptance by biologists of predictions made with molecular dynamics simulations of biomolecules. Its purpose is to increase the awareness of biologists of the contribution that simulations can make to our understanding of biomolecule function.

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Article Information

DOI

10.1002/ijch.201400074

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© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

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Keywords

  • computational chemistry;
  • molecular dynamics;
  • molecular simulations;
  • nucleic acids;
  • proteins

Publication History

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  • Version of record online:
  • Manuscript Received:
  • Manuscript Accepted:

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  3. 3Giuliano Malloci, Giovanni Serra, Andrea Bosin, Attilio Vargiu, Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case, Computation, 2016, 4, 1, 5CrossRef
  4. 4Matías R. Machado, Sergio Pantano, SIRAH tools: mapping, backmapping and visualization of coarse-grained models, Bioinformatics, 2016, 32, 10, 1568CrossRef
  5. 5You Xu, Alexander D. MacKerell, Lennart Nilsson, Structural effects of modified ribonucleotides and magnesium in transfer RNAs, Bioorganic & Medicinal Chemistry, 2016CrossRef
  6. 6Giuliano Malloci, Attilio Vargiu, Giovanni Serra, Andrea Bosin, Paolo Ruggerone, Matteo Ceccarelli, A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds, Molecules, 2015, 20, 8, 13997CrossRef
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