tag:blogger.com,1999:blog-2909827059962062852.post387120541362691793..comments2024-03-26T17:10:36.305+00:00Comments on Molecular Design: The homeopathic limit of ligand efficiencyPeter Kennyhttp://www.blogger.com/profile/12180360326821860667noreply@blogger.comBlogger2125tag:blogger.com,1999:blog-2909827059962062852.post-3405844527843482702016-01-02T14:57:23.043+00:002016-01-02T14:57:23.043+00:00Hi Dan, All the best for the 2016.
As a point of ...Hi Dan, All the best for the 2016.<br /><br />As a point of clarification, I have never suggested that free energy (or IC50 values) are not useful. When we use these quantities to compare activity/affinity, we can usually assume that the same standard/reference concentration applies to all measurements and so meaningful (and useful) comparisons can be made. If you do sensible things with free energies (like subtract them from each other) things will go smoothly but things will unravel quickly should you break the rules. If your view of a system changes when you change a unit of a quantity that specifies the system then it’s a clear sign that you’ve broken the rules and playing the ‘useful card’ will not (in a Monopoly sense) get you out of jail.<br /><br />One needs to be very careful about invoking ‘useful’ in defense of metrics (and scientific concepts in general) because it’s a subjective term that some may even equate with the last refuge of the scoundrel. Is it possible to say whether LE defined using 1 M standard state is more useful than LE defined with a 100 mM standard state? Is LELP useful? Are the thermodynamic proxies that were skewered in an earlier <a href="http://fbdd-lit.blogspot.com/2015/10/voodoo-thermodynamics-for-dummies.html" rel="nofollow">post</a> useful? The problem with ‘useful’ is that anyone can claim that a metric is useful.Peter Kennyhttps://www.blogger.com/profile/12180360326821860667noreply@blogger.comtag:blogger.com,1999:blog-2909827059962062852.post-65431099892260811242016-01-01T17:43:45.546+00:002016-01-01T17:43:45.546+00:00Of course, these arguments also apply to binding f...Of course, these arguments also apply to binding free energy, which people nonetheless find useful.<br /><br />And the Tolkien allusion was made previously in <a href="http://practicalfragments.blogspot.com/2013/04/one-metric-to-rule-them-all.html" rel="nofollow">this post</a>, and extended poetically by Brandon Findlay in one of the comments. Happy 2016!Dan Erlansonhttps://www.blogger.com/profile/07927082337051189270noreply@blogger.com