Release Notes

v2.5.0 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.

PDB Blast Search¶

This module defines functions for blast searching the Protein Data Bank.

class PDBBlastRecord(xml=None, sequence=None, **kwargs)[source]¶

A class to store results from blast searches.

Instantiate a PDBBlastRecord object instance.

Parameters:	xml (str) – blast search results in XML format or an XML file that contains the results sequence (str) – query sequence

fetch(xml=None, sequence=None, **kwargs)[source]¶

Get Blast record from url or file.

Parameters:	sequence (`Atomic`, `Sequence`, str) – an object with an associated sequence string or a sequence string itself xml (str) – blast search results in XML format or an XML file that contains the results or a filename for saving the results or None timeout (int) – amount of time until the query times out in seconds default value is 120

getBest()[source]¶: Returns a dictionary containing structure and alignment information for the hit with highest sequence identity.

getHits(percent_identity=0.0, percent_overlap=0.0, chain=False)[source]¶

Returns a dictionary in which PDB identifiers are mapped to structure and alignment information.

Parameters:

Parameters:	percent_identity (float) – PDB hits with percent sequence identity equal to or higher than this value will be returned, default is `0.` percent_overlap (float) – PDB hits with percent coverage of the query sequence equivalent or better will be returned, default is `0.` chain (bool) – if chain is True, individual chains in a PDB file will be considered as separate hits, default is False

percent_identity (float) – PDB hits with percent sequence identity equal to or higher than this value will be returned, default is 0.
percent_overlap (float) – PDB hits with percent coverage of the query sequence equivalent or better will be returned, default is 0.
chain (bool) – if chain is True, individual chains in a PDB file will be considered as separate hits, default is False

getParameters()[source]¶: Returns parameters used in blast search.

getSequence()[source]¶: Returns the query sequence that was used in the search.

writeSequences(filename, **kwargs)[source]¶

Writes a fasta file containing the hit sequences under ‘hseq’ field. These are not equivalently aligned.

Arguments of getHits can be parsed as kwargs.

blastPDB(sequence, filename=None, **kwargs)[source]¶

Returns a PDBBlastRecord instance that contains results from blast searching sequence against the PDB using NCBI blastp.

Parameters:	sequence (`Atomic`, `Sequence`, str) – an object with an associated sequence string or a sequence string itself filename (str) – a filename to save the results in XML format

hitlist_size (default is 250) and expect (default is 1e-10) search parameters can be adjusted by the user. sleep keyword argument (default is 2 seconds) determines how long to wait to reconnect for results. Sleep time is multiplied by 1.5 when results are not ready. timeout (default is 120 s) determines when to give up waiting for the results.