[ccp4bb] Postdoctoral position at the European Institute of Oncology, Milano

Postdoctoral research position in Structural Biology of Asymmetric Cell Division A postdoctoral research position is available in the group of Marina Mapelli at the European Institute of Oncology in Milano. The main interest of the group focuses on the molecular mechanisms underlying asymmetric

Re: [ccp4bb] Ligand binding protein partner search

Hi, Predict_FX has worked quite well in our hands for that purpouse but you have to pay for a licence. It is currently commercialized by Certara: http://www.certara.com/products/molmod/predictfx Regards, Zsolt Böcskei sanofi Paris 2013/10/14 Rose, Peter > You may use similarity to known lig

[ccp4bb] postdoctoral position on structural biology at UW-Madison

You are invited to apply for a postdoctoral position in the structural biology lab of McArdle Cancer Institute of University of Wisconsin at Madison. We are interested in understanding the structural basis and mechanisms of cancer-related cell signaling proteins and protein complexes. One importa

Re: [ccp4bb] High Rsyms between 5-7 A

Dear Ursula, I wouldnt be worried too much abot 4.4% Rsym to be honest. At this high redundancy rather look on Rpim. I once had a case with a low I/sI medium resolution shell where I had strong translational NCS. Is this the case? Go publish! Best, Matthias

Re: [ccp4bb] High Rsyms between 5-7 A

Here is some more info on the data: lowest res. shell (50-8.0A): Rsym=4.4%, I/sig=100. detector ADSC315, 1 degree oscillations, mosaicity around 0.3 The Rsym stays high whether I merge just the first 30 frames or 200 frames. Wouldn't that speak against radiation damage? The crystals were grown f

[ccp4bb] High Rsyms between 5-7 A

I have a data set with high Rsym in the lower resolution ranges, and I don't understand what is going on. The crystal diffracts to about 3.0 A and has large cell dimension ( space group P6522 a= 185., c= 360.) Mosaicity is low. I processed the data in P6522, solved the structure and refined it. T

Re: [ccp4bb] Ligand binding protein partner search

You may use similarity to known ligands to find potential binding partners in the PDB. Try a ligand similarity search for your ligand: http://www.rcsb.org/pdb/search/advSearch.do From the menu, choose “Chemical Structure” and draw your ligand. Then select “Search Type: Similar”. This search wil

Re: [ccp4bb] Ligand binding protein partner search

It's definitely possible to rig, say, autodock to run the same small molecule over every protein in the PDB. Results, of course, should be taken with a grain of salt. On Mon, 2013-10-14 at 20:53 +0900, L wrote: > Hi all, > > > I'm looking for a way to find/predict protein partner(s) for our > l

Re: [ccp4bb] Off-topic: Correlation of crystallographic B factors with NMR relaxation parameters

Florian, B-factors will likely correlate with any property that changes depending on the distance from protein surface. Whether such correlation means causation is always difficult to prove. Cheers, Ed. -- "I'd jump in myself, if I weren't so good at whistling."

[ccp4bb] nano-crystals

Dear CCP4bb, We recently published a paper on collecting high resolution cryo-EM data of submicron (± 100 nm) 3D lysozyme crystals.(doi:10.1107/S0907444913002734 ). We are working hard to develop tools that can be used to interpret this data. In the m

[ccp4bb] Ligand binding protein partner search

Hi all, I'm looking for a way to find/predict protein partner(s) for our ligand (small chemical; MW<500 Da). There're lots of servers and softwares to find/predict a ligand with known protein structure, but hardly find a way to discover potential protein partner(s) with known ligand. That would

Re: [ccp4bb] Off-topic: Correlation of crystallographic B factors with NMR relaxation parameters

Hi Florian, I haven't done this but would like to comment on the generally interesting idea. If the NMR data are measured on the same crystal form, I would expect a general correlation between both parameters. The absolute scale of B factors from different resolutions will vary, but you s

Re: [ccp4bb] Rfree stuck

Just a word of warning - 1) you cant really compare R factors between twinned and untwinned refinements - they are calculated differently. 2) If the data is twinned the Free R set needs to be selected in the higher symmetry Laue group and expanded so that twinned pairs are either both in the Free