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Extracting the Dynamic Motion of Proteins Using Normal Mode Analysis

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Data Mining Techniques for the Life Sciences

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2449))

Abstract

Normal mode analysis (NMA) is a technique for describing the conformational states accessible to a protein in a minimum energy conformation. NMA gives results similar to those produced by principal components analysis of a molecular dynamics simulation, but with only a fraction of the computational effort. Here, we provide a brief overview of the theory and describe three methods for carrying out NMA, including the use of one of the on-line services, the use of off-line software for calculating the projection of the modes calculated from one conformation onto another, and an all-atom NMA calculated using GROMACS. For all three methods, we will use the E1·2Ca2+ form of the Ca2+-ATPase as a concrete example.

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Acknowledgment

The authors would like to thank Eva Kutejová for general support during the writing of this chapter.

This work was supported by a grant from the Scientific Grant Agency of the Ministry of Education, Science, Research, and Sport of the Slovak republic (VEGA) [2/0131/20] and by the Interreg V-A Slovakia-Austria program (https://www.sk-at.eu/) for the project StruBioMol, ITMS: 305011X666 which is co-financed by the European Regional Development Fund.

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Authors and Affiliations

  1. Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia

    Jacob A. Bauer & Vladena Bauerová-Hlinková

Authors
  1. Jacob A. Bauer
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  2. Vladena Bauerová-Hlinková
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Corresponding author

Correspondence to Jacob A. Bauer .

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Editors and Affiliations

  1. University of Pavia, Pavia, Italy

    Oliviero Carugo

  2. Genome Institute and Bioinformatics Institute, Singapore, Singapore

    Frank Eisenhaber

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Bauer, J.A., Bauerová-Hlinková, V. (2022). Extracting the Dynamic Motion of Proteins Using Normal Mode Analysis. In: Carugo, O., Eisenhaber, F. (eds) Data Mining Techniques for the Life Sciences. Methods in Molecular Biology, vol 2449. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2095-3_9

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  • DOI: https://doi.org/10.1007/978-1-0716-2095-3_9

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2094-6

  • Online ISBN: 978-1-0716-2095-3

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