DynamicDistances
[source]¶Bases: object
Dynamic distance calculator
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. |
Examples
>>> DynamicDistances.cutoff('A', 'Y')
9.121
>>> DynamicDistances.percentile('A', 'Y')
0.443
Methods
cutoff (x, y) |
Return the amino acid pair-specific cB-cB cutoff |
percentile (x, y) |
Return 95-97 percentile data |
RosettaFunctionConstructs
[source]¶Bases: object
Storage for string formats of different Rosetta energy function constructs
Attributes: |
|
---|
BOUNDED_default
¶Simple bounded energy function
BOUNDED_gremlin
¶Energy function according to [2]
References
[2] | (1, 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] | (1, 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. |
[4] | (1, 2) 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] | (1, 2) Michel et al. (2014). PconsFold: improved contact predictions improve protein models. Bioinformatics 30(17), i482-i488 |
SIGMOID_default
¶Simple sigmoidal energy function