Hello to everyone,
I am working on the modeling of a class of FMN-dependent NAD(P)H enzymes, where FMN is tightly bound to the protein. Interaction Fingerprints (IF) seems to be a powerfull tool to convert complex 3D-data (eg. a binding pocket) into more menageable, and easier to compare 1D-bit strings. Free-Maestro works well for this purpose but it seems that the IF were calculated only for the ligand-protein couple and not for FMN. In the workspace the first entry is the FMN-protein and the second is the ligand. How can I compute IF for the ligand-protein-FMN complex as if FMN were considered like a residue that belongs to the protein?
Thank you in advance for your attention,
Nicola Porta
Dear Sir,
I am an user of Schrodinger. Interactions with prosthetic groups NAD, FMN cannot be visualized in the interaction finger print diagram as such because the amino acids we visualize in the IF diagram are of those of the active site. However, The programme cannot recognize FMN as an amino acid. Instead, you can try to visualize the interactions on workspace or 2D interaction diagram.
Thank you.
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