Protein Structure¶

PDB resources¶

• fetchPDB() - retrieve PDB files
• fetchPDBviaFTP() - download PDB/PDBML/mmCIF files
• fetchPDBviaHTTP() - download PDB files

You can use following functions to manage PDB file resources:

• pathPDBFolder() - local folder for storing PDB files
• pathPDBMirror() - local PDB mirror path
• wwPDBServer() - set wwPDB FTP/HTTP server for downloads

Following functions can be used to handle local PDB files:

• findPDBFiles() - return a dictionary containing files in a path
• iterPDBFilenames() - yield file names in a path or local PDB mirror

Blast search PDB¶

The following are for blast searching PDB content.

• blastPDB() - blast search NCBI PDB database
• PDBBlastRecord - store/evaluate NCBI PDB blast search results

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.

• listPDBCluster() - get list of identifiers in a PDB sequence cluster
• loadPDBClusters() - load PDB clusters into memory
• fetchPDBClusters() - retrieve PDB sequence cluster data from wwPDB

Parse/write PDB files¶

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

• parsePDB() - parse .pdb formated file
• parsePDBStream() - parse .pdb formated stream
• writePDB() - write .pdb formatted file
• writePDBStream() write .pdb formated stream

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

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:

• assignSecstr() - add secondary structure data from header to atoms
• buildBiomolecules() - build biomolecule from 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:

• fetchPDBLigand() - retrieve ligand from Ligand-Expo

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:

• getAlignmentMethod(), setAlignmentMethod()
• getMatchScore(), setMatchScore()
• getMismatchScore(), setMismatchScore()
• getGapPenalty(), setGapPenalty()
• getGapExtPenalty(), setGapExtPenalty()

Execute DSSP¶

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

• execDSSP() - execute dssp
• performDSSP() - execute dssp and parse results
• parseDSSP() - parse structural data from dssp output

Execute STRIDE¶

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

• execSTRIDE() - execute stride
• performSTRIDE() - execute stride and parse results
• parseSTRIDE() - parse structural data from stride output