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Analyzing Biomolecular Ensembles

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Biomolecular Simulations

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

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Abstract

Several techniques are available to generate conformational ensembles of proteins and other biomolecules either experimentally or computationally. These methods produce a large amount of data that need to be analyzed to identify structure–dynamics–function relationship. In this chapter, we will cover different tools to unveil the information hidden in conformational ensemble data and to guide toward the rationalization of the data. We included routinely used approaches such as dimensionality reduction, as well as new methods inspired by high-order statistics and graph theory.

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Acknowledgments

This work was supported by two ISCRA-CINECA HPC Grants (NetDyn-HP10C2TOOC and ALLO-PCM-HP10CWP9KW) and two EU-PRACE DECI projects DECI-13th and DECI-14th and DeiC Pilot Project in 2016–2017 on a Danish Infrastructure Computerome. EP group is supported by LEO Foundation Grant 2017–2019 (grant number LF17006), Alfred Benzon Investigator Fellowships 2017–2019, a DFF-FNU grant from the Danish Council of Independent Research (grant number 7014-00272B), and Carlsberg Foundation Distinguished Fellowship (grant number CF18-0314). EP group is also part of the Center of Excellence for Autophagy, Recycling and Disease funded by Danmarks Grundforskningsfond (grant number DNRF125).

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  1. Matteo Lambrughi and Matteo Tiberti contributed equally to this work.

Authors and Affiliations

  1. Computational Biology Laboratory, Danish Cancer Society Research Center, Copenhagen, Denmark

    Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth, Juan Salamanca Viloria, Emmanuelle Bignon & Elena Papaleo

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  1. Matteo Lambrughi
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  2. Matteo Tiberti
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  3. Maria Francesca Allega
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  7. Juan Salamanca Viloria
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  8. Emmanuelle Bignon
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  9. Elena Papaleo
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Correspondence to Elena Papaleo .

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Editors and Affiliations

  1. Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

    Massimiliano Bonomi

  2. Dipartimento di Bioscienze, UniversitĂ  degli Studi di Milano, Milano, Italy

    Carlo Camilloni

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Lambrughi, M. et al. (2019). Analyzing Biomolecular Ensembles. In: Bonomi, M., Camilloni, C. (eds) Biomolecular Simulations. Methods in Molecular Biology, vol 2022. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9608-7_18

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  • DOI: https://doi.org/10.1007/978-1-4939-9608-7_18

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