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 The SeqProp Class and The StructProp Class pages.

Protein structure predictions

Homology modeling

Transmembrane orientations

Kinetic folding rate

Protein structure calculations

Secondary structure

Solvent accessibilities

Residue depths

Structural similarity

Various structure properties

Structure cleaning, mutating

Protein sequence predictions

Secondary structure

Solvent accessibilities


Transmembrane domains

Aggregation propensity

Protein sequence calculations

Various sequence properties

Sequence alignment