Database Support

This module contains features for accessing databases containing protein related data.

Pfam

The following functions can be used to search and retrieve Pfam data:

UniProt

The following functions and class can be used to search and retrieve UniProt data:

  • queryUniprot() - query UniProt and parse the results as a dictionary
  • UniprotRecord - a wrapper from UniProt data with functions including parsing PDBs
  • searchUniprot() - search UniProt and return a UniprotRecord

CATH

The following class and its functions can be used to search and retrieve CATH data:

  • CATHDB - parse, handle and navigate the tree-like structure of the CATH database

DALI

The following class and functions can be used to search and retrieve data using the DALI structure alignment server:

QuartataWeb

The following classes and functions can be used to search and retrieve data using the QuartataWeb structure alignment server:

Gene Ontology Annotation (GOA)

The following classes and functions can be used to search and retrieve data from the EBI GOA database:

Interpro

The following functions can be used to search and retrieve Interpro data:

  • searchInterpro() - search for domain families of a protein

BioExcel-CV19

The following functions can be used to retrieve BioExcel-CV19 data:

  • fetchBioexcelPDB() - fetch PDB files for starting structures for trajectories