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:

fetchPfamMSA() - download MSA files

searchPfam() - search for domain families of a protein

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:

searchDali() - search for similar structures using DALI

DaliRecord - fetch and handle outputs from DALI searches

daliFilterMultimers() - filter DALI results to obtain multimers of a particular size

QuartataWeb

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

QuartataWebBrowser - class based on the Splinter web browser package to search QuartataWeb

QuartataChemicalRecord - class to handle the outputs of QuartataWeb searches

searchQuartataWeb() - perform QuartataWeb searches and return the output in a QuartataChemicalRecord

Gene Ontology Annotation (GOA)

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

queryGOA() - query GOA using a PDB ID

GOADictList - class to handle data from GOA queries

parseOBO() - parse an OBO file containing the Gene Ontology.

parseGAF() - parse a Gene Association File (GAF)

showGoLineage() - visualize GO tree

calcGoOverlap() - Calculate overlap between GO terms from their distance in the graph

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