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