[ccp4bb] CCPBioSim Industry Talk - 10 July

2024-06-27 Thread Sarah Fegan - STFC UKRI
Dear all, Registration is now open for our next industry talk on 10 July 2024 at 2pm UK time. The talk by Steve Maginn, Chemical Computing Group / Molecular Graphics and Modelling Society, has the title "At the Interface of Academia and Industry for 35 Years... (aka - "You get less time for m

[ccp4bb] cc minor off topic protein symmetry

2024-06-27 Thread Andrew Lovering
Many thanks to Mark van Raaij for a super example - 5EFV - clear heterogeneity at the hinge/kink; although this then doesn't return to the 1st axis Its interesting to contemplate proteins doing this several times in a physiologically "real" way (the models I'm looking at do this) - they need gly

Re: [ccp4bb] Good electron density but poor affinity

2024-06-27 Thread Tanner, John
The refined crystallographic occupancy (sort of a measure of electron density quality) has been related to the ligand binding constant. In this study, they determined several structures of a protein with different concentrations of the ligand. The binding constant was estimated from a plot of th

[ccp4bb] cc - minor off topic protein symmetry

2024-06-27 Thread Andrew Lovering
(I should note that my use of symmetry is used on the protein level rather on the absolute crystallographic equivalence level - imagine this trimer sat within a P1 cell, and that minor wobbles generate pseudosymmetry in places anyway - what I'm interested in is the topology of the chain at the j

[ccp4bb] Good electron density but poor affinity

2024-06-27 Thread Armando Albert
Dear all, Is there any study that analyzes the relationship between the quality of the electron density of a ligand and its affinity? Armando To unsubscribe from the CCP4BB list, click the following link: https://www.jiscma

[ccp4bb] minor off topic protein symmetry

2024-06-27 Thread Andrew Lovering
Dear wise list, I have a question regarding protein oligomers that have multiple, differing axes of symmetry - stimulated by some perplexing but likely real Alphafold models. I think it's the protein equivalent of this old chestnut: https://en.wikipedia.org/wiki/Three_utilities_problem Consid