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College of Engineering and Computing


Biomedical Engineering

Structure Calculation From RDCs

Proteins are a type of macromolecules that perform important functions within the body. Characterizing the structure of a given protein is often a requisite step in discovery of its particular function. Some diseases cause mutations in certain proteins which can cause "misfolding" and lead to disfunction. Therefore, knowing the structure of a protein can lead to a better understanding of the causes of these diseases and inform intelligent drug design to combat them. In our lab we use the software REDCRAFT to fold proteins from Residual Dipolar Couplings (RDCs) to study their structures. Our approach utilizes only 2% of the experimental data required for traditional methods of structure determination while reducing the computational requirement of protein folding problem to a polynomial time complexity.

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Publications

  • Casey A. Cole, D. Ishimaru, M. Hennig, H. Valafar. (2016). Structure Calculation of α,Α/β, β Proteins From Residual Dipolar Coupling Data Using Redcraft. In: H. R. Arabnia, Q. N. Tran (Eds.), Emerging Trends in Applications and Infrastructures for Computational Biology, Bioinformatics, and Systems Biology. Morgan Kaufmann, Imprint of Elsevier, Cambridge, MA, pp. 73–88
  • Simin, M., Irausquin, S., Cole, C. A., Valafar, H. (2014). Improvements to REDCRAFT: a software tool for simultaneous characterization of protein backbone structure and dynamics from residual dipolar couplings. Journal of Biomolecular NMR. http://doi.org/10.1007/s10858-014-9871-x, PMID: 25403759