Hi -
A RDKit-based implementation of the QED measure as described by
Richard Bickerton (Nature Chemistry, 2012, 4, 90-98) has been
implemented and made available for download from our website ( www.silicos-it.com > Biscu-it).
Regards,
- Hans
Hi Hans,
Thanks for the implementation!
Why did you use your own 11 smarts for hydrogen bond acceptors instead of rdkit's CalcNumHBA or NumHAcceptors ($([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),$([nH0,o,s;+0]))?
I compared your implementation with PipelinePilot and rdkit, and it correlates better with PP (r^2=0.978) than rdkit (0.916). Maybe Greg you can comment on this?
(In PipelinePilot, HBA is described as "number of heteroatoms (Oxygen, Nitrogen, Sulfur, or Phosphorus) with one or more lone pairs, excluding atoms with positive formal charges, amide and pyrrole-type Nitrogens, and aromatic Oxygen and Sulfur atoms in heterocyclic rings")
On your website, you mention that "discrepancies can be noted in the results from the logP calculations"; I agree that the end result won't be much different using MolLogP vs. ALogP.
But to be consistent I collected the structures of the 771 drugs mentioned in the original publication, calculated their MolLogP using rdkit, and fitted the binned distribution using the described approach.
700 compounds out of 771 gave the same ALogP as listed in the original paper (i.e. same structure), however for the 71 remaining drugs some discrepancies were observed, maybe due to different structures (I collected them from PubChem) or a different version of Pipeline Pilot (I used version 8.5).
I ended up with a bin size of 0.97 and the following parameters:
a
0.486849448
b
186.2293718
c
2.066177165
d
3.902720615
e
1.027025453
f
0.913012565
Dmax
145.43148
Feel free to use them!
Best,
Grégori
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