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

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

The 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

Parse mmCIF files

Following ProDy functions are for parsing .cif files:

parseMMCIF() - parse .cif formated file

parseMMCIFStream() - parse .cif formated stream

Quick visualization

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

Edit structures

The 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

Analyze interactions and stability with InSty and find water bridges with WatFinder

Use the following to analyze interactions within protein structure or between protein and ligand structure in single PDB file or in trajectory:

addHydrogens() - add missing hydrogens to .pdb files

calcHydrogenBonds() - compute hydrogen bonds in proteins

calcSaltBridges() - compute salt bridges in proteins

calcRepulsiveIonicBonding() - compute repulsive ionic bonding in proteins

calcPiStacking() - compute Pi-stacking interactions in proteins

calcPiCation() - compute Pi-cation interactions in proteins

calcHydrophobic() - compute hydrophobic interactions in proteins

calcProteinInteractions() - compute all above interaction types at once

showProteinInteractions_VMD() - return TCL file for visualization in VMD

calcHydrogenBondsDCD() - compute hydrogen bonds in a trajectory for proteins

calcSaltBridgesDCD() - ompute salt bridges in a trajectory for proteins

calcRepulsiveIonicBondingDCD() - compute repulsive ionic bonding in a trajectory for proteins

calcPiStackingDCD() - compute Pi-stacking interactions in a trajectory for proteins

calcPiCationDCD() - compute Pi-cation interactions in a trajectory for proteins

calcHydrophobicDCD() - compute hydrophobic interactions in a trajectory for proteins

calcStatisticsInteractions() - return statistical information for each interaction type

calcLigandInteractions() - compute all type of interactions between protein and ligand

listLigandInteractions() - return list of interactions between protein and ligand

showLigandInteraction_VMD() - return TCL file for visualization of interactions for VMD

Interactions - store inteactions for a single PDB structure

InteractionsDCD - store interactions for a trajectory

Detect channels, tunnels and pores with CaviFinder

Use the following to analyze cavities within protein structures in single PDB file or in trajectory:

getVmdModel() - generates a 3D model of proten, using VMD, which is then use for visualization

calcChannels() - computes and identifies channels

calcChannelsMultipleFrames() - compute channels for each frame in a given trajectory or PDB ensemble

getChannelParameters() - extracts and returns the lengths, bottlenecks, and volumes of each channel

getChannelAtoms() - generates an AtomGroup object representing the atoms along the paths of the given channels

showChannels() - visualizes the channels using Open3D

showCavities() - visualizes the cavities using Open3D

Compare/align chains

The 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

The following functions can be used to adjust alignment parameters:

getAlignmentMethod(), setAlignmentMethod()

getMatchScore(), setMatchScore()

getMismatchScore(), setMismatchScore()

getGapPenalty(), setGapPenalty()

getGapExtPenalty(), setGapExtPenalty()

Execute DSSP

The 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

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

execSTRIDE() - execute stride

parseSTRIDE() - parse structural data from stride output

performSTRIDE() - execute stride and parse results

Handle EMD Map Files and Build Pseudoatoms into them

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

parseEMD() - parse structural data from .emd files

EMDMAP - access structural data from .emd files

TRNET - fit pseudoatoms to EM density maps using the TRN algorithm

Add missing atoms including hydrogens

Use the following to add missing atoms

addMissingAtoms() - add missing atoms with separately installed OpenBabel or PDBFixer

Missing residues can also be added if a PDB or mmCIF file with SEQRES entries is provided.