DynamicDistances
[source]¶Bases: object
Dynamic distance calculator
The data stored in this class corresponds to Supplementary Table 3 in [1].
Examples
>>> DynamicDistances.cutoff('A', 'Y')
9.121
>>> DynamicDistances.percentile('A', 'Y')
0.443
References
[1] | Kamisetty et al. (2013). Assessing the utility of coevolution based residue-residue contact predictions in a sequence and structure rich era. PNAS 110(39), 15674-9. |
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 [2]_
References
[2] | Ovchinnekov et al. (2015). Large-scale determination of previously unsolved protein structures using evolutionary information. Elife 3(4), e09248. |
FADE
¶Energy function according to [3] and [4]_
References
[3] | 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. |
[4] | 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 |
FLAT_HARMONIC
¶ROSETTA FLAT_HARMONIC energy function
GAUSSIAN
¶Simple Gaussian energy function
SIGMOID_default
¶Simple sigmoidal energy function