26 June 2011

Ligand efficiency and related metrics (Poll)

The discussion following the recent post on LLEAT got me thinking that metrics could be a good topic for a poll (see right side of page).

Click below to see definitions or references, and vote on the right side of the page. Note that you can choose multiple answers.
Antibacterial efficiency
Binding efficiency index (BEI)
Fit quality (FQ)
Ligand efficiency (LE)
Ligand-efficiency-dependent lipophilicity (LELP)
Ligand lipophilic efficiency (LLE)
Percentage efficiency index (PEI)
Surface-binding efficiency index (SEI)

Also, if you use any additional metrics or want to be more specific about how or why you use (or don’t use) the above metrics, please comment.


Peter Kenny said...

Good initiative, Dan! It's been flagged up in the new FB group.

I actually use pIC50/N(HevAtom) for LE rather than converting it to units of free energy since units are often not reported (can lead to speakers being embarrassed when asked about the units of the quantities on which they're pontificating).

I also use pIC50-ClogP and prefer not to use the term Ligand-Lipophilicity Efficiency because (a) I was using pIC50-ClogP before it got christened LLE (b) the term sounds silly and (c) the people who proposed the term actually say that it can be defined using ClogP or logD (which means that, like the Ro3 hydrogen bond acceptors, LLE is not actually defined well enough for you to know exactly what the term describes).

Dan Erlanson said...

Thanks Pete!

I thought about including your metrics (BES and BEL) but the list was getting pretty long already, and I wasn't sure whether you'd settled on formal names and definitions.

I agree that people are often sloppy about units, let alone ClogP and logD or IC50 and Ki, but personally I like having something that feels like a thermodynamic parameter, illusory though it may be.

Peter Kenny said...

Good decision, Dan. I think nomenclature is a real problem in the efficiency metric field and I don't think that my suggestions represented much of an improvement. Actually I'm starting to take the view that the best solution would be to use the function itself (e.g. pIC50 - ClogP) rather than using names that can mean different things.

Vladimir Chupakhin said...

Thinking about making a slides for students.