Hello, > I've just released http://code.google.com/p/pyplif/ PyPLIF , a Python-based > Protein-Ligand Interaction Fingerprinting which is using Open Babel library.
Great - I've been using the Marcou's C++ program. Works fine. I don't use it so often, but I'll look at your version and try it when I have some time - I'm not a good programmer, but it's, as you said, much easier for me with python... I personnaly use Surflex or Flexx outpout (actually only site.mol2 + poses.mol2). Were you able to reproduce the results from the Marcou's paper? What do you think of an additionnal score for comparing new ligands to the reference? Let's say the reference has 2 interactions, and that you have a new ligand with exactly the same 2 interactions and a third interaction: this ligand would have a lower tanimoto score, but it would be interesting to know that all reference interactions are still reproduced. And what about giving different weights to different types of interaction? E.g. 2 reference interactions: one H-bond and one hydrophobic. One ligand with only the H bond. One other ligand with only the hydrophobic contact. Same tanimoto coefficient for the 2 ligands. But in my opinion the ligand with the polar interaction would be more interesting. Any thought about that? Regards, Pascal ------------------------------------------------------------------------------ Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
