This section will give an overview of the methods that can be executed for the Protein class, which is a basic representation of a protein by a collection of amino acid sequences and 3D structures.
.. toctree:: :glob: :maxdepth: 1 notebooks/Protein*
- Load, parse, and store the same (ie. from different database sources) or similar (ie. from different strains) protein sequences as :ref:`SeqProp <sequence>` objects in the :attr:`~ssbio.core.protein.Protein.sequences` attribute
- Load, parse, and store multiple experimental or predicted protein structures as :ref:`StructProp <structure>` objects in the :attr:`~ssbio.core.protein.Protein.structures` attribute
- Set a single :attr:`~ssbio.core.protein.Protein.representative_sequence` and :attr:`~ssbio.core.protein.Protein.representative_structure`
- Calculate, store, and access pairwise sequence alignments to the representative sequence or structure
- Provide summaries of alignments and mutations seen
- Map between residue numbers of sequences and structures
.. automodule:: ssbio.core.protein
:members:
For examples in which tools from the Protein class have been used for analysis, please see the following:
| [1] | Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, et al. Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis. Proc Natl Acad Sci U S A. 2016;113: E8344–E8353. doi:10.1073/pnas.1613446113 |
| [2] | Mih N, Brunk E, Bordbar A, Palsson BO. A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PLoS Comput Biol. 2016;12: e1005039. doi:10.1371/journal.pcbi.1005039 |