tag:blogger.com,1999:blog-1136153439451224584.post5303495963160170997..comments2024-03-27T06:45:59.174-07:00Comments on Practical Fragments: Fragment docking: promiscuous but good enough?Dr. Teddy Zhttp://www.blogger.com/profile/07288045760981372367noreply@blogger.comBlogger3125tag:blogger.com,1999:blog-1136153439451224584.post-25579955160790441112012-03-30T09:22:53.025-07:002012-03-30T09:22:53.025-07:00Thanks Teddy,
I completely agree, but sometimes m...Thanks Teddy,<br /><br />I completely agree, but sometimes modelers present only their best pose rather than an ensemble of best poses, particularly in publications. It might make sense for computational chemists to treat their models more like those that come out of NMR than those that come out of X-ray. <br /><br />I do think it would be fun to throw NMR, X-ray, and modeling at a single target and see whether NMR and modeling are able to capture more of the dynamics than X-ray, and Pim-1 seems like it might be a good candidate, though I suppose it is getting a bit large for NMR.Dan Erlansonhttps://www.blogger.com/profile/07927082337051189270noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-36986897647008940352012-03-30T06:44:53.780-07:002012-03-30T06:44:53.780-07:00Dan, I think it is not necessarily that the dockin...Dan, I think it is not necessarily that the docking forces a single binding mode, but that Xray only has one binding mode. Proteins are dynamic; NMR structures reports the ensemble of structures. In the past, I have worked on a project where all 40 ensemble NMR structures were used in the docking, it captured some interesting modes for binding.Dr. Teddy Zhttps://www.blogger.com/profile/07288045760981372367noreply@blogger.comtag:blogger.com,1999:blog-1136153439451224584.post-14526740012322016972012-03-29T07:45:55.819-07:002012-03-29T07:45:55.819-07:00This comment has been removed by a blog administrator.Anonymousnoreply@blogger.com