Dear James > I actually chose 3dko because it is a kinase (with a ligand), and > therefore an interesting candidate for a molecular replacement > "score". I have not set this up yet, but I think if you look for PDB > entries that contain the word "kinase" and try to molecular-replace > all of them into the 3dko dataset, what fraction of them will "work"? > I think that fraction would make a good "score" for a given molecular > replacement pipeline.
At the recent CCP4 SW in Nottingham Giovanna Scapin from Merck gave a talk on MR during which she reflected upon their attempts from some time ago to troubleshoot a recalcitrant MR case of a kinase by searching with hunderds of models derived from all kinase structures known at that time. However, I am not quite sure if they published these results anywhere (at least I could not fish out a relevant reference). Along these lines, 'Wide Search MR' (Stokes-Rees and Sliz (2010) PNAS 107: 21476-21481) and (www.sbgrid.org) may also provide some options to establish such benchmarking or MR 'scores'. Best regards Savvas > > > On Mon, Jan 14, 2013 at 2:31 PM, Nat Echols <nathaniel.ech...@gmail.com> > wrote: >> On Mon, Jan 14, 2013 at 11:18 AM, Tim Gruene <t...@shelx.uni-ac.gwdg.de> >> wrote: >>> I admit not having read all contributions to this thread. I understand >>> the "John Henry Challenge" as whether there is an 'automated way of >>> producing a model from impossible.mtz'. From looking at it and without >>> having gone all the way to a PDB-file my feeling is one could without >>> too much effort from the baton mode in e.g. coot. >> >> This should be even more possible if one also uses existing knowledge >> about the expected structure of the protein: a kinase domain is quite >> distinctive. So, James, how much external information from homologous >> structures are we allowed to use? Running Phaser would certainly be >> cheating, but if I take (for instance) a 25% identical kinase >> structure, manually align it to the map and/or a partial model, and >> use that as a guide to manually rebuild the target model, does that >> meet the terms of the challenge? >> >> -Nat
