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The StructProp Class

The StructProp Class

Introduction

This section will give an overview of the methods that can be executed for a single protein structure.

Tutorials

notebooks/StructProp* notebooks/PDBProp* notebooks/FATCAT*

Available functions

Sequence & structure-based predictions

Function Description Internal Python class
used and functions provided		 External software
to install		 Web server Alternate external
software to install
Homology modeling Preparation scripts and parsers for
executing homology modeling algorithms
  • itasserprep module <ssbio.protein.structure.homology.itasser.itasserprep>
  • itasserprop module <ssbio.protein.structure.homology.itasser.itasserprop>
 instructions/itasser
Transmembrane
orientation		 Prediction of transmembrane domains and
orientation in a membrane		 opm module <ssbio.protein.structure.properties.opm> instructions/opm
Kinetic folding rate Prediction of protein folding rates
from amino acid sequence		 kinetic_folding_rate module <ssbio.protein.sequence.properties.kinetic_folding_rate> instructions/foldrate

Structure-based calculations or functions

Function Description Internal Python class
used and functions provided		 External software
to install		 Web server Alternate external
software to install
Secondary structure Calculations of secondary structure
  • Biopython DSSP
  • dssp module <ssbio.protein.structure.properties.dssp>
  • stride module <ssbio.protein.structure.properties.stride>
 instructions/dssp instructions/stride
Solvent accessibilities Calculations of per-residue absolute and
relative solvent accessibilities
  • Biopython DSSP
  • dssp module <ssbio.protein.structure.properties.dssp>
  • freesasa module <ssbio.protein.structure.properties.freesasa>
 instructions/dssp instructions/freesasa
Residue depths Calculations of residue depths instructions/msms
Structural similarity Pairwise calculations of 3D structural
similarity		 fatcat module <ssbio.protein.structure.properties.fatcat> instructions/fatcat
Various structure
properties		 Basic properties of the structure, such
as distance measurements between residues
or number of disulfide bridges
  • Biopython Struct
  • structure residues module <ssbio.protein.structure.properties.residues>
Quality Custom functions to allow ranking of
structures by percent identity to a defined
sequence, structure resolution, and other structure
quality metrics		 set_representative_structure function <ssbio.core.protein.Protein.set_representative_structure>
Structure cleaning,
mutating		 Custom functions to allow for the preparation
of structure files for molecular modeling, with
options to remove hydrogens/waters/heteroatoms,
select specific chains, or mutate specific residues.
  • Biopython Select
  • cleanpdb module <ssbio.protein.structure.utils.cleanpdb>
  • mutatepdb module <ssbio.protein.structure.utils.mutatepdb>
 AmberTools

API

ssbio.protein.structure.structprop