conkit.misc.energyfunction module

Energy function templates for restraint generation

class RosettaFunctionConstructs[source]

Bases: object

Storage for string formats of different Rosetta energy function constructs

For more information on the different energy functions, please refer to the corresponding references or the official RosettaCommons documentation

BOUNDED_default

Simple bounded energy function

BOUNDED_gremlin

Energy function according to [1]

References

[1]Ovchinnekov et al. (2015). Large-scale determination of previously unsolved protein structures using evolutionary information. Elife 3(4), e09248.
FADE

Energy function according to [2] and [3]

References

[2]Simkovic et al. (2016). Residue contacts predicted by evolutionary covariance extend the application of ab initio molecular replacement to larger and more challenging protein folds. IUCrJ 3(Pt 4), 259-270.
[3]Michel et al. (2014). PconsFold: improved contact predictions improve protein models. Bioinformatics 30(17), i482-i488
FADE_default

Energy function according to [4]

References

[4]Michel et al. (2014). PconsFold: improved contact predictions improve protein models. Bioinformatics 30(17), i482-i488
SIGMOID_default

Simple sigmoidal energy function

SIGMOID_gremlin

Energy function according to [5]

References

[5]Ovchinnekov et al. (2015). Large-scale determination of previously unsolved protein structures using evolutionary information. Elife 4, e09248.