Abstract
Despite the significant increase in computational power, molecular modeling of protein structure using classical all-atom approaches remains inefficient, at least for most of the protein targets in the focus of biomedical research. Perhaps the most successful strategy to overcome the inefficiency problem is multiscale modeling to merge all-atom and coarse-grained models. This chapter describes a well-established CABS coarse-grained protein model. The CABS (C-Alpha, C-Beta, and Side chains) model assumes a 2–4 united-atom representation of amino acids, knowledge-based force field (derived from the statistical regularities seen in known protein sequences and structures) and efficient Monte Carlo sampling schemes (MC dynamics, MC replica-exchange, and combinations). A particular emphasis is given to the unique design of the CABS force-field, which is largely defined using one-dimensional structural properties of proteins, including protein secondary structure. This chapter also presents CABS-based modeling methods, including multiscale tools for de novo structure prediction, modeling of protein dynamics and prediction of protein–peptide complexes. CABS-based tools are freely available at http://biocomp.chem.uw.edu.pl/tools
The original version of this chapter was revised. The erratum to this chapter is available at: DOI 10.1007/978-1-4939-6406-2_21
An erratum to this chapter can be found at http://dx.doi.org/10.1007/978-1-4939-6406-2_21
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Acknowledgments
Funding for this work was provided by the National Science Center grant [MAESTRO 2014/14/A/ST6/00088] and by the Foundation for Polish Science TEAM project (TEAM/2011-7/6) cofinanced by the EU European Regional Development Fund operated within the Innovative Economy Operational Program.
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Kmiecik, S., Kolinski, A. (2017). One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model. In: Zhou, Y., Kloczkowski, A., Faraggi, E., Yang, Y. (eds) Prediction of Protein Secondary Structure. Methods in Molecular Biology, vol 1484. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6406-2_8
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DOI: https://doi.org/10.1007/978-1-4939-6406-2_8
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