Converts an apo protein structure into a receptor. The active site is identified by a ligand residue specified by the user (-site_residue). The residue is used as a hint to select most appropriate active site from a list of potential active sites generated by a shape algorithm that searches for pockets/grooves and cavities.
Converts PDB file 3E1X containing an apo protein into a receptor using residue TRP215B to identify the active site.
- 3E1X.pdb.gz : PDB file to convert into a receptor.
prompt> apopdb2receptor -pdb 3E1X.pdb.gz -site_residue TRP215B
- receptor.oeb.gz : Receptor version of 3E1X.
A description of the command line interface can be obtained by executing ApoPdb2Receptor with the --help option.
> apopdb2receptor --help
will generate the following output:
Help functions: apopdb2receptor --help simple : Get a list of simple parameters apopdb2receptor --help all : Get a complete list of parameters apopdb2receptor --help defaults : List the defaults for all parameters apopdb2receptor --help <parameter> : Get detailed help on a parameter apopdb2receptor --help html : Create an html help file for this program apopdb2receptor --help versions : List the toolkits and versions used in the application
A file of an apo protein to be converted into a receptor file. Typically this will be a PDB file, however any molecular format with residue information can be used (e.g., OEBinary).
The active site must not contain a bound ligand. Use Pdb2Receptor to convert a protein-ligand complex into a receptor file.
[ Aliases = -in ]
The name of a residue near the active site of the protein. Residue names can be of the following forms.
|<Residue Name><Residue Number>||HIS1034|
|<Residue Name><Residue Number><Chain ID>||HIS1034A|
If the residue naming is not specific enough and matches multiple residues in the pdb file the program will list the available, more specific, options to choose from.
[ Aliases = -site ]
A list of one or more residue names associated with solvent molecules in the pdb file.
Molecules that have a residue matching one of these names will be stripped from the protein structure and stored in the receptor as extra molecules (i.e., they will have no effect on docking and scoring).
The default setting of this flag (HOH) strips waters from the protein. To not strip any molecules specify this flag as ‘NoSolvents’.
[ Aliases = -solvent ]