Paul Emsley wrote: > On 17/09/10 07:57, markus kossner wrote: > >> some time ago I implemented a filter function during a pdb mining >> campaign. The Idea was to exclude compounds to far away from drug like >> chemical matter. >> >> > > As a matter of interest, how did you convert from a pdb file that might > contain a ligand to an RDKit mol? Look for residues with HETATMs? In > making the RDKit mol, how did you know the bonds and the bond orders > (look them up in the Chemical Component Library, perhaps)? (non-trivial > AFAICS). > > Paul. > > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > Ehm, I think Greg has already said the right comment some days ago when he wrote that he would not even dare to try this. Neither did I ... I used the entries in the scPdb database. There you can download the Protein in pdb and the corresponding ligand as mol2. This makes things a lot easier with small molecule pdb ligands ... Then you can handle the protein with biopython and do the small molecule stuff using RDKit. Markus
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