| Bioinformatics Toolbox | |
Retrieve protein structure data from PDB database
Data = getpdb('PDBid',
'PropertyName', PropertyValue...)
getpdb(..., 'ToFile', ToFileValue)
getpdb(..., 'MirrorSite', MirrorSiteValue)
PDBid | Unique identifier for a protein structure record. Each structure in the PDB is represented by a 4-character alphanumeric identifier. For example, 4hhb is the identification code for hemoglobin. |
ToFile | Property to specify the location and filename for saving data. Enter either a filename or a path and filename supported by your system (ASCII text file). |
MirrorSite | Property to select Web site. Enter either http://rutgers.rcsb.org/pdb to use the Rutgers University Web site, or enter http://nist.rcsb.org/pdb for the National Institute of Standards and Technology site. |
getpdb retrieves sequence information from the Protein Data Bank. This database contains 3-D biological macromolecular structure data.
Data = getpdb('PDBid', 'PropertyName',PropertyValue...) searches for the ID in the PDB database and returns a MATLAB structure containing the following fields:
Header Title Compound Source Keywords ExperimentData Authors Journal Remark1 Remark2 Remark3 Sequence HeterogenName HeterogenSynonym Formula Site Atom RevisionDate Superseded Remark4 Remark5 Heterogen Helix Turn Cryst1 OriginX Scale Terminal HeterogenAtom Connectivity
getpdb(..., 'ToFile', ToFileValue) saves the data returned from the database to a file. Read a PDB formatted file back into MATLAB using the function pdbread.
getpdb(...,'MirrorSite', MirrorSiteValue) allows you to choose a mirror site for the PDB database. The default site is the San Diego Supercomputer Center, http://www.rcsb.org/pdb. See http://www.rcsb.org/pdb/mirrors.html for a full list of PDB mirror sites.
Retrieve the structure information for the electron transport (heme protein) with PDB ID 5CYT.
pdbstruct = getpdb('5CYT')
Bioinformatics Toolbox functions getembl, getgenbank, getgenpept, getpir, pirread
| | getnodesbyid (biograph) | getpir | |
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