Saturday, February 9, 2008

Resolving Conflicts in More than One Complex in the Same PFam Family

if there were two known complexes in the same pfam family, how did you use the combined information. And if homologs
were involved, did you just assign the aligned residues to the interface based on what interfacial residues were identified in the x-ray structure.

If we have known yeast complexes, this always takes precedent over any information in iPfam. If there is an interaction between two proteins known which share one Pfam domain _and_ the Pfam domain has been shown to bind itself in a crystal structure (i.e. in iPfam), we annotate that these two proteins will bind each other through the interface that is seen in that structure. In the
case of asymmetric binding between the same domain, the assignment is ad hoc. Ad II.) Yes, we use Pfam assignments as a form of homology mapping. We then assign the interface based on what is seen in the crystal structure.

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