This notebook contains material from PyRosetta; content is available on Github.

Structure Refinement

One of the most basic operations in protein structure and design algorithms is manipulation of the protein conformation. In Rosetta, these manipulations are organized into movers. A Mover object simply changes the conformation of a given pose. It can be simple, like a single φ or ψ angle change, or complex, like an entire refinement protocol.

Suggested Reading

  • P. Bradley, K. M. S. Misura & D. Baker, “Toward high-resolution de novo structure prediction for small proteins,” Science 309, 1868-1871 (2005), including Supplementary Material.
  • Z. Li & H. A. Scheraga, “Monte Carlo-minimization approach to the multiple-minima problem in protein folding,” Proc. Natl. Acad. Sci. USA 84, 6611-6615 (1987).

https://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshop5_StructureRefinement.pdf

https://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshops_Appendix_A.pdf

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Chapter contributors:

  • Kathy Le (Johns Hopkins University); this chapter was adapted from the PyRosetta book (J. J. Gray, S. Chaudhury, S. Lyskov, J. Labonte).