Pyrosetta Resources

Guide

https://docs.rosettacommons.org/docs/latest/getting_started/I-want-to-do-x#docking

Energy terms

https://docs.rosettacommons.org/docs/latest/rosetta_basics/scoring/score-types

https://docs.rosettacommons.org/docs/latest/rosetta_basics/scoring/centroid-score-terms

Movers

https://docs.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Movers/movers_pages/PyMolMover

FAQ

https://docs.rosettacommons.org/docs/latest/getting_started/FAQ

initcommands(Important)

https://docs.rosettacommons.org/docs/latest/full-options-list

Namespace

https://docs.rosettacommons.org/manuals/archive/rosetta_3.8_user_guide/all_else/d2/d2a/namespacepyrosetta.html

Resfile syntax

https://docs.rosettacommons.org/docs/latest/rosetta_basics/file_types/resfiles

Operations

https://graylab.jhu.edu/PyRosetta.documentation/pyrosetta.rosetta.core.pack.task.operation.html

Selectors

https://docs.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/ResidueSelectors/ResidueSelectors#residueselectors_conformation-independent-residue-selectors_chainselector

Citations

FastRelax Mover’s citation(s):

*Tyka MD, *Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, and Baker D. (2011). Alternate states of proteins revealed by detailed energy landscape mapping. J Mol Biol 405(2):607-18. doi: 10.1016/j.jmb.2010.11.008. (*Co-primary authors.)

Khatib F, Cooper S, Tyka MD, Xu K, Makedon I, Popovic Z, Baker D, and Players F. (2011). Algorithm discovery by protein folding game players. Proc Natl Acad Sci USA 108(47):18949-53. doi: 10.1073/pnas.1115898108.

Maguire JB, Haddox HK, Strickland D, Halabiya SF, Coventry B, Griffin JR, Pulavarti SVSRK, Cummins M, Thieker DF, Klavins E, Szyperski T, DiMaio F, Baker D, and Kuhlman B. (2021). Perturbing the energy landscape for improved packing during computational protein design. Proteins 89(4):436-449. doi: 10.1002/prot.26030.