Tagged questions

What are the biggest differences in solving NMR structures of DNA or RNA vs. proteins?

2 1 13238
answers votes views
I've only solved NMR structure of globular proteins (actually in a complex with a short stretch of DNA), but never a str...
Justin Frank 1 Jun 27 '16 at 19:27

Generate inter-proton distance restraints from an X-ray structure

1 1 4k
answers votes views
Hello, Does anyone know of any program that can generate inter-proton distance restraints from an X-ray structure? I w...
Josef Chmelik 1 May 07 '13 at 05:33

How would you compare solving NMR structure of a smaller peptide vs that of globular protein?

2 0 19348
answers votes views
By smaller peptide I mean somewhere around 15-20 aminoacids, having a cycle or two that constrain the geometry. Also - ...
SankarampadiAravamudhan 91 Mar 17 '11 at 01:01

cs23d vs. cs-rosetta

2 1 6k
answers votes views
Does anybody have any thoughts on this ? I dont really know which is better, CS23D or CS-ROSETTA. Clearly they are ide...
Thomas Garner 81 Jan 19 '11 at 08:05

How to keep XPLOR structure calculation from exploding?

1 0 4k
answers votes views
Trying to calculate a structure using sa.inp script and the energy in the cooling loop increases instead of going down. ...
Evgeny Fadeev 5771 Nov 02 '10 at 11:57

How to assign (perturbed) resonances when structure is known?

1 0 5k
answers votes views
I had two problems like this one recently: have protein (in solution) of known general structure resonance assignments...
Aleksandr Yakimov 11 Apr 25 '10 at 01:17

Is there a tool to manage NOE and other restraint lists for the structure calculations?

1 0 5k
answers votes views
Hello, I'm currently working on solving a peptide NMR solution structure using NIH-XPLOR. I find myself a lot starting ...
Ilango 171 Apr 02 '10 at 05:45

Software to model a 9-mer peptide that binds divalent metals and may oligomerize?

1 1 11607
answers votes views
I'm gearing up for a project in which we're looking at the structure of a short peptide that should fold upon binding di...
Evgeny Fadeev 5771 Mar 18 '10 at 09:32

How do you use PyMol to visualize structure bundles and related MR data?

0 0 7k
answers votes views
Hello, are you using pymol to analyze NMR structures? (I've been mostly using Molmol before). Have you learned any PyMo...
Evgeny Fadeev 5771 Mar 02 '10 at 12:29

How do you find incorrectly assigned NOE restraints?

3 1 7k
answers votes views
So you've analyzed your NOE data sets and have 1000+ assigned restraints, with probably inevitable errors. Going through...
Evgeny Fadeev 5771 Mar 02 '10 at 09:09

Are there alternatives to MOLMOL for visualization of NMR structure ensemebles?

2 0 5k
answers votes views
Hi folks, I've been using Molmol, but found significant issues when working with a non-standard structure. For example...
Evgeny Fadeev 5771 Mar 02 '10 at 08:05

How to display NMR structure of molecule with non-standard residues?

1 0 11729
answers votes views
... solving a structure of a cyclic peptide with Ornithine residue, where Orn side-chain participates in an amide bond. ...
Evgeny Fadeev 5771 Feb 02 '10 at 08:59

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