| Bioinformatics Toolbox | |
Read data from Protein Data Bank (PDB) file
PDBData = pdbread('File')
File | Protein Data Bank (PDB) formatted file (ASCII text file). Enter a filename, a path and filename, or a URL pointing to a file. File can also be a MATLAB character array that contains the text for a PDB file. |
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional protein structures. pdbread reads data from a PDB formatted file into MATLAB.
PDBData = pdbread('File') reads the data in PDB formatted text file File and stores the data in the MATLAB structure PDBData.
The data stored in each record of the PDB file is converted, where appropriate, to a MATLAB structure. For example, the ATOM records in a PDB file are converted to an array of structures with the following fields: AtomSerNo, AtomName, altLoc, resName, chainID, resSeq, iCode, X, Y, Z, occupancy, tempFactor, segID, element, and charge.
The sequence information from the PDB file is stored in the Sequence field of PDBData. The sequence information is itself a structure with the fields NumOfResidues, ChainID, ResidueNames, and Sequence. The field ResidueNames contains the three-letter codes for the sequence residues. The field Sequence contains the single-letter codes for the sequence. If the sequence has modified residues, then the ResidueNames might not correspond to the standard three-letter amino acid codes, in which case the field Sequence will contain a ? in the position corresponding to the modified residue.
For more information about the PDB format, see
http://www.rcsb.org/pdb/docs/format/pdbguide2.2/ guide2.2_frame.html
Get information for the human hemoglobin protein with number 1A00 from the Protein Data Bank, store information in the file collagen.pdb, and then read the file back into MATLAB.
getpdb( '1A00','ToFile', 'collagen.pdb')
pdbdata = pdbread('collagen.pdb')
Bioinformatics Toolbox functions genpeptread, getgenpept, getpdb, pirread
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