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Protein Structure Prediction Using Coarse-Grained Models

  • Maciej Blaszczyk
  • Dominik Gront
  • Sebastian Kmiecik
  • Mateusz Kurcinski
  • Michal Kolinski
  • Maciej Pawel Ciemny
  • Katarzyna Ziolkowska
  • Marta Panek
  • Andrzej KolinskiEmail author
Chapter
Part of the Springer Series on Bio- and Neurosystems book series (SSBN, volume 8)

Abstract

The knowledge of the three-dimensional structure of proteins is crucial for understanding many important biological processes. Most of the biologically relevant protein systems are too large for classical, atomistic molecular modeling tools. In such cases, coarse-grained (CG) models offer various opportunities for efficient conformational sampling and thus prediction of the three-dimensional structure. A variety of CG models have been proposed, each based on a similar framework consisting of a set of conceptual components such as protein representation, force field, sampling, etc. In this chapter we discuss these components, highlighting ideas which have proven to be the most successful. As CG methods are usually part of multistage procedures, we also describe approaches used for the incorporation of homology data and all-atom reconstruction methods.

Notes

Acknowledgements

Maciej Blaszczyk, Sebastian Kmiecik, Katarzyna Ziolkowska and Marta Panek acknowledge support from Foundation for Polish Science TEAM project (TEAM/2011-7/6) co-financed by the European Regional Development Fund operated within the Innovative Economy Operational Program. We also acknowledge support from the National Science Center (NCN Poland) Grant (MAESTRO2014/14/A/ST6/00088).

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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Maciej Blaszczyk
    • 1
  • Dominik Gront
    • 1
  • Sebastian Kmiecik
    • 1
  • Mateusz Kurcinski
    • 1
  • Michal Kolinski
    • 2
  • Maciej Pawel Ciemny
    • 1
    • 3
  • Katarzyna Ziolkowska
    • 1
  • Marta Panek
    • 1
  • Andrzej Kolinski
    • 1
    Email author
  1. 1.Faculty of Chemistry, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
  2. 2.Bioinformatics LaboratoryMossakowski Medical Research Centre, Polish Academy of SciencesWarsawPoland
  3. 3.Faculty of PhysicsUniversity of WarsawWarsawPoland

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