Release Notes

v2.4.1 series come with new and improved sequence, structure, and dynamics analysis features. See release notes for details.

How to Cite

Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments
Bioinformatics 2011 27(11):1575-1577.

Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics
Bioinformatics 2014 30(18):2681-2683.

Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python
Bioinformatics 2021 37(20):3657-3659.

Pfam Access Functions¶

This module defines functions for interfacing Pfam database.

searchPfam(query, **kwargs)[source]¶

Returns Pfam search results in a dictionary. Matching Pfam accession as keys will map to evalue, alignment start and end residue positions.

Parameters:	query (str) – UniProt ID or PDB identifier with or without a chain identifier, e.g. `'1mkp'` or `'1mkpA'`. UniProt ID of the specified chain, or the first protein chain will be used for searching the Pfam database timeout (int) – timeout for blocking connection attempt in seconds, default is 60

fetchPfamMSA(acc, alignment='seed', compressed=False, **kwargs)[source]¶

Returns a path to the downloaded Pfam MSA file.

Parameters:

Parameters:	acc (str) – Pfam ID or Accession Code alignment – alignment type, one of `'full'`, `'seed'` (default), `'ncbi'`, `'metagenomics'`, `'rp15'`, `'rp35'`, `'rp55'`, `'rp75'` or `'uniprot'` where rp stands for representative proteomes. InterPro Pfam seems to only have seed alignments easily accessible in most cases compressed – gzip the downloaded MSA file, default is False timeout – timeout for blocking connection attempt in seconds, default is 60 outname (str) – out filename, default is input `'acc_alignment.format'` folder (str) – output folder, default is `'.'`

acc (str) – Pfam ID or Accession Code
alignment – alignment type, one of 'full', 'seed' (default), 'ncbi', 'metagenomics', 'rp15', 'rp35', 'rp55', 'rp75' or 'uniprot' where rp stands for representative proteomes. InterPro Pfam seems to only have seed alignments easily accessible in most cases
compressed – gzip the downloaded MSA file, default is False
timeout – timeout for blocking connection attempt in seconds, default is 60
outname (str) – out filename, default is input 'acc_alignment.format'
folder (str) – output folder, default is '.'

parsePfamPDBs(query, data=[], **kwargs)[source]¶

Returns a list of AtomGroup objects containing sections of chains that correspond to a particular PFAM domain family. These are defined by alignment start and end residue numbers.

Parameters:

Parameters:	query (str) – Pfam ID, UniProt ID or PDB ID If a PDB ID is provided the corresponding UniProt ID is used. If this returns multiple matches then start or end must also be provided. This query is also used for label refinement of the Pfam domain MSA. data (list) – If given the data list from the Pfam mapping table will be output through this argument. start (int) – Residue number for defining the start of the domain. The PFAM domain that starts closest to this will be selected. Default is 1 end (int) – Residue number for defining the end of the domain. The PFAM domain that ends closest to this will be selected.

query (str) – Pfam ID, UniProt ID or PDB ID If a PDB ID is provided the corresponding UniProt ID is used. If this returns multiple matches then start or end must also be provided. This query is also used for label refinement of the Pfam domain MSA.
data (list) – If given the data list from the Pfam mapping table will be output through this argument.
start (int) – Residue number for defining the start of the domain. The PFAM domain that starts closest to this will be selected. Default is 1
end (int) – Residue number for defining the end of the domain. The PFAM domain that ends closest to this will be selected.