software.rst

Index: Software

This section provides a simple list of external software that may be required to carry out specific computations on a protein sequence or structure. This list only contains software that is wrapped with ssbio -- there may be other programs that carry out these same functions, and do it better (or worse)!

Tables describing functionalities of these software packages in relation to their input, as well as links to internal wrappers and parses are found on :ref:`sequence` and :ref:`structure` pages.

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Protein structure predictions

Homology modeling

.. toctree::
    :maxdepth: 1

    instructions/itasser

Transmembrane orientations

.. toctree::
    :maxdepth: 1

    instructions/opm

Kinetic folding rate

.. toctree::
    :maxdepth: 1

    instructions/foldrate

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Protein structure calculations

Secondary structure

.. toctree::
    :maxdepth: 1

    instructions/dssp
    instructions/stride

Solvent accessibilities

.. toctree::
    :maxdepth: 1

    instructions/dssp
    instructions/freesasa

Residue depths

.. toctree::
    :maxdepth: 1

    instructions/msms

Structural similarity

.. toctree::
    :maxdepth: 1

    instructions/fatcat

Various structure properties

• :mod:`structure residues module <ssbio.protein.structure.properties.residues>`

Quality

• :func:`set_representative_structure function <ssbio.core.protein.Protein.set_representative_structure>`

Structure cleaning, mutating

• :mod:`cleanpdb module <ssbio.protein.structure.utils.cleanpdb>`
• :mod:`mutatepdb module <ssbio.protein.structure.utils.mutatepdb>`

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Protein sequence predictions

Secondary structure

.. toctree::
    :maxdepth: 1

    instructions/scratch

Solvent accessibilities

.. toctree::
    :maxdepth: 1

    instructions/scratch

Thermostability

• :mod:`thermostability module <ssbio.protein.sequence.properties.thermostability>`

Transmembrane domains

.. toctree::
    :maxdepth: 1

    instructions/tmhmm

Aggregation propensity

.. toctree::
    :maxdepth: 1

    instructions/amylpred

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Protein sequence calculations

Various sequence properties

.. toctree::
    :maxdepth: 1

    EMBOSS pepstats <instructions/emboss>

Sequence alignment

.. toctree::
    :maxdepth: 1

    EMBOSS needle <instructions/emboss>