Protein Structure

This module defines classes and functions to fetch, parse, and write structural data files, execute structural analysis programs, and to access and search structural databases, e.g. ProteinDataBank.

PDB resources

You can use following functions to manage PDB file resources:

Following functions can be used to handle local PDB files:

Blast search PDB

The following are for blast searching PDB content.

PDB clusters biopolymer chains using blast weekly. These clusters can be retrieved using the following functions. Using cluster data is as good as blast searching PDB most of the time and incredibly faster always.

Parse/write PDB files

Following ProDy functions are for parsing and writing .pdb files:

Since .pqr format is similar to .pdb format, following functions come as bonus features:

  • writePQR() - write atomic data to a file in .pqr format
  • parsePQR() - parse atomic data from files in .pqr format

See also

Atom data (coordinates, atom names, residue names, etc.) parsed from PDB/PSF/PQR/mmCIF files are stored in AtomGroup instances. See atomic module documentation for more details.

Parse mmCIF files

Following ProDy functions are for parsing .cif files:

  • parseCIF() - parse .cif formated file
  • parseCIFStream() - parse .cif formated stream

See also

Atom data (coordinates, atom names, residue names, etc.) parsed from PDB/PSF/PQR/mmCIF files are stored in AtomGroup instances. See atomic module documentation for more details.

Quick visualization

showProtein() function can be used to take a quick look at protein structures.

Edit structures

Following functions allow editing structures using structural data from PDB header records:

PDB header data

Use the following to parse and access header data in PDB files:

  • parsePDBHeader() - parse header data from .pdb files
  • Chemical - store PDB chemical (heterogen) component data
  • Polymer - store PDB polymer (macromolecule) component data
  • DBRef - store polymer sequence database reference records

Ligand data

Following function can be used to fetch meta data on PDB ligands:

Compare/align chains

Following functions can be used to match, align, and map polypeptide chains:

  • matchChains() - finds matching chains in two protein structures
  • matchAlign() - finds best matching chains and aligns structures
  • mapOntoChain() - maps chains in a structure onto a reference chain

Following functions can be used to adjust alignment parameters:

Execute DSSP

Following functions can be used to execute DSSP structural analysis program and/or parse results:

Execute STRIDE

Following functions can be used to execute STRIDE structural analysis program and/or parse results:

Execute EMD

Following functions can be used to execute EMDMAP structural analysis program and/or parse results: