tag:blogger.com,1999:blog-1136153439451224584.post1579528687479090080..comments2024-03-27T06:45:59.174-07:00Comments on Practical Fragments: Ligand efficiency and related metrics (Poll)Dr. Teddy Zhttp://www.blogger.com/profile/07288045760981372367noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-1136153439451224584.post-88066283366461546752011-07-14T06:51:17.657-07:002011-07-14T06:51:17.657-07:00Thinking about making a slides for students.Thinking about making a slides for students.Vladimir Chupakhinhttps://www.blogger.com/profile/14838130425318070954noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-19596018436613480312011-07-01T09:17:43.503-07:002011-07-01T09:17:43.503-07:00Good decision, Dan. I think nomenclature is a rea...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.Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-86369718197999087082011-06-30T21:52:06.795-07:002011-06-30T21:52:06.795-07:00Thanks Pete!
I thought about including your metri...Thanks Pete!<br /><br />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. <br /><br />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.Dan Erlansonhttps://www.blogger.com/profile/07927082337051189270noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-35024775083772833962011-06-29T14:05:34.578-07:002011-06-29T14:05:34.578-07:00Good initiative, Dan! It's been flagged up in...Good initiative, Dan! It's been flagged up in the new FB group.<br /><br />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). <br /><br />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).Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.com