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Re: [modeller_usage] Modeling ligands in the binding site

Qinghua Liao wrote:
I want to build a model with a ligand in the binding sites, but I have problems. I read the manual on-line, but I don't find any python script for aligning the sequence to the structure with ligand. I don't know the differences when compared to structure without ligand. Could somebody give me some example of these python script, or give me some suggestion on how to edit the python script which is used to align to structure without ligand? Thanks very much!

Typically you would do a regular alignment of your structure (without ligand) against the target sequence, then manually edit the alignment file to add ligand(s). Since ligands are simply copied directly from the template to the target, the alignment in this region is simply 1:1, so it is comparatively easy to add manually. And relying on a conventional sequence alignment algorithm to generate this alignment is asking for trouble, since most algorithms use a distance matrix (e.g. BLOSUM) that only contains distances for the standard amino acids, not for the full range of possible ligands.

	Ben Webb, Modeller Caretaker
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