AutoLigand:(1) identification of a receptor's ligand binding site


It is suggested to start AutoLigand through the GUI that the autodocktools provide. autoligand r FileBaseName -p #_of_pts The above is a simplification provided for the Debian package. The regular command line invocation is through python /usr/share/pyshared/AutoDockTools/ -r FileBaseName -p #_of_pts


autoligand is a symbolic link to the Python script That performs a an automated investigation of the likelihood of a particular part of a protein to bind to ligands.
Description of command...
-r FileBaseName = just the name part from receptor map files (i.e.,
-p #_of_pts = number of fill points to use (int)
Note: can be omitted if -a option used.
Optional parameters:
[-a #] = number of heavy atom for ligand (#_of_pts will be set to 6x atoms) [-x # -y # -z #] = optional x,y,z co-ords for starting fill (float)
when starting point is input, only one fill will be run
[-i # -j # -k #] = optional x,y,z co-ords for second point (float)
when second point is input, the fill will connect both points NOTE: the connection path has not been optimized - use with discretion
[-f #] = number of fills to generate - default is 10 [-e] = use the extra atom types NA, N, SA, and A
NOTE: these results can be problematic - use with discretion
[-m] = make a movie of output fill progress


Rodney M. Harris and colleagues at The Scripps Institute, San Diego, California