Hi Koustav, I had the same question before and here is the answer from Eugene Krissinel, the developer of PISA:
"Yes PISA has a database of compounds, which contains certain interaction parameters. If a compound is not found in the database, then PISA does not know how it interacts with other molecules and for this the compound is ignored. The only way to repair this is to process your compound, which cannot be done until it is deposited to our database. But even then, I am afraid, nothing can be done because I am no longer with the EBI and full knowledge of PISA was not digested by people left behind. Sorry for the crude truth." Good luck, Matt 2009/11/25 Koustav Maity <mai...@gmail.com> > Hi All, > I am using MSD PISA web server to analyze the protein ligand interface in > my newly solved structure. The ligand in the structure is a new inhibitor > (generated using PRODRG), so there is no entry for the inhibitor in the PDB. > Therefore when I am uploading my pdb file to PISA server it is not > recognizing the ligand molecule. Probably PISA reads the ligand identifier > and matches with the database to process it as a ligand. Is there any way I > can specify my inhibitor library file ? or is there some other way to > resolve this issue? > Koustav > -- -------------------------------------------------------------------------------------------- Matthew L.H. Chu, PhD The University of Manchester, UK --------------------------------------------------------------------------------------------
