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Data Mining of Macromolecular Structures

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Data Mining Techniques for the Life Sciences

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1415))

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Abstract

The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

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Acknowledgments

This work was supported by VIDI grant 723.013.003 from the Netherlands Organisation for Scientific Research (NWO).

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Authors and Affiliations

  1. Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands

    Bart van Beusekom, Anastassis Perrakis & Robbie P. Joosten

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  1. Bart van Beusekom
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  2. Anastassis Perrakis
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  3. Robbie P. Joosten
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Correspondence to Robbie P. Joosten .

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  1. Max F. Perutz Laboratories GmbH, Universität Wien, Wien, Austria

    Oliviero Carugo

  2. Technology and Research (A*STAR), Agency for Science, Singapore, Singapore

    Frank Eisenhaber

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van Beusekom, B., Perrakis, A., Joosten, R.P. (2016). Data Mining of Macromolecular Structures. In: Carugo, O., Eisenhaber, F. (eds) Data Mining Techniques for the Life Sciences. Methods in Molecular Biology, vol 1415. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3572-7_6

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  • DOI: https://doi.org/10.1007/978-1-4939-3572-7_6

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