similarity_SPLIF Question

[Justine Camilla Williams]

Hello Dr. Wójcikowski,

 

I had emailed you earlier with a SPLIF inquiry. I hope you don’t mind if I ask you a question about the similarity_SPLIF function.

 

When I compared two identical SPLIF fingerprints using similarity_SPLIF, the value that was returned was around 0.6. Since these two protein-ligand complexes, and thus fingerprints were exactly the same, I expected a value of 1.0, which is what I got when I compared using the interaction, and simple_interaction functions.

 

I was reading through the reference article associated with SPLIF and it sounded like I should be getting a normalized result, but I was not sure if I had misunderstood this. Could you please let me know if my result makes sense?

 

I really appreciate your help with this. Thank you very much!

 

Justine

[Maciek Wójcikowski]

Dear Justine,

SPLIF is non-standard fingerprint, as FP usually are invariant to 3d orientation. In contrast SPLIF contains additional 3D location of bits, thus to compare poses in different binding pockets you need to make sure that they are properly aligned in 3D. You can do that with most modelling software, like UCSF Chimera or Schrodinger's Maestro. If that doesn't work and you can share the protein/ligand files, please send them to me so I can check what is the problem.

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Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

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