Is there any thing the funding agencies can do?
Sridhar On 8/10/2011 3:50 PM, Dale Tronrud wrote:
Oops! My bond length rmsd was 0.106 not 0.160 A. Still unacceptable but not quite as bad. Sorry, Dale Tronrud On 08/10/11 15:45, Dale Tronrud wrote:I've made a quick look at the model and the paper - and it doesn't need more than a quick look. The description of the model in the paper sounds great. The problems in the model are clear. My favorite is the quote "Trp-477 of PTH1R makes several van der Waals contacts with Trp-339 and Lys-337 of G-beta-1 ...". They are "contacts" all right. The distances between the 477:CH2 and 337:CE is 2.75 A and between 477:NE1 and 339:CH2 is 2.26 A. There are many more. In general the geometry of this entire model is terrible. In Table 1 the bond length rmsd is listed at 1.64 A and the bond angles are 0.0078 deg! Perhaps one is to presume the numbers should be swapped. In any case, the values I calculate for the model are 0.160 A and 4.46 deg! Absolutely dreadful. The PDB header lists the (swapped) values from the paper and then reports hundreds of outliers. The tools proposed by the Validation Task Force should cause a model like this to pop out clearly. Even the old tools show this model is quite unreliable. We just have to use them. Dale Tronrud On 08/10/11 14:35, Jacob Keller wrote:On the surface it doesn't seem as bad as others, i.e., it does not seem to be a real fake--perhaps just a strong form of wishful thinking and creative density interpretation. I wonder what would be a good metric in which to establish a cutoff for present/not present in density. CC, maybe? Jacob On Wed, Aug 10, 2011 at 4:01 PM, David Schuller<dj...@cornell.edu> wrote:Time to fuel up the gossip engines for the approaching weekend: http://www.sciencedirect.com/science/article/pii/S096921260800186X RETRACTED: Structure of the Parathyroid Hormone Receptor C Terminus Bound to the G-Protein Dimer Gβ1γ2 Structure, Volume 16, Issue 7, 9 July 2008, Pages 1086-1094 Structure 2QNS withdrawn. -- ======================================================================= All Things Serve the Beam ======================================================================= David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
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