SHIFTX2: Chemical Shift Prediction
SHIFTX2 website
SHIFTX2 is capable of rapidly and accurately calculating diamagnetic 1H, 13C and 15N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain...
gwnmr
NMR software
0
01-10-2012 06:13 PM
[NMR software blog] Spinus and nmrdb.org
Spinus and nmrdb.org
I don't remember how many years ago I discovered the web. I was excited by how many things were available for free. There were a lot of curious and interesting things but, I was the first to admit, nothing really serious that could substitute a true book, or a true CD or a true computer program. The great thing about the internet was that I could easily read the opinions of other people around the world. I mean: ordinary people just like me.Things began to change with the appearance of SDBS 14 years ago. It was the first really useful thing I found on the web.The last...
nmrlearner
News from NMR blogs
0
06-17-2011 02:54 PM
[NMRpipe Yahoo group] Re: problems in linear prediction for both indirect diemnsions in CC
Re: problems in linear prediction for both indirect diemnsions in CC
Dear Frank, * Thank you very much for your help. * It worked now. The main change*as you suggested is from * * ... to * ... * for both indirect
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NMRpipe Yahoo group news
News from other NMR forums
0
02-16-2011 09:34 PM
[NMRpipe Yahoo group] Re: problems in linear prediction for both indirect diemnsions in CC
Re: problems in linear prediction for both indirect diemnsions in CC
Dear Frank, * Thank you very much for going through the script and pointing out*several places need to be corrected or checked out. I will follow what you
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NMRpipe Yahoo group news
News from other NMR forums
0
02-16-2011 09:34 PM
4D prediction of protein 1H chemical shifts
4D prediction of protein 1H chemical shifts
Abstract A 4D approach for protein 1H chemical shift prediction was explored. The 4th dimension is the molecular flexibility, mapped using molecular dynamics simulations. The chemical shifts were predicted with a principal component model based on atom coordinates from a database of 40 protein structures. When compared to the corresponding non-dynamic (3D) model, the 4th dimension improved prediction by 6â??7%. The prediction method achieved RMS errors of 0.29 and 0.50 ppm for Hα and HN shifts, respectively. However, for individual proteins...
nmrlearner
Journal club
0
01-09-2011 12:46 PM
[NMR software blog] Routine Prediction
Routine Prediction
Not everybody remembers how easy it is and how effective it can be to add (or correct) a few points at the beginning of the FID. Two years ago I explained how Linear Prediction works and how we can extrapolate the FID in both directions. This time I will show a simple practical application.
I have observed that, in recent years, C-13 spectra acquired on Varian instruments require a much-larger-then-it-used-to-be phase correction. When I say correction, I mean first-order phase correction, because the zero-order correction is merely a different way of representing the...
nmrlearner
News from NMR blogs
0
12-01-2010 08:36 PM
A Guide to Structure Prediction, by Rob Russell
A Guide to Structure Prediction (version 2.1) (link)
Rob Russel (for EMBL) gives a useful, step-by-step guide to predicting 3D protein structure, and provides links to numerous online resources. An excerpt from the website is pasted below.
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Introduction
This is by no means intended to be a comprehensive guide to predicting protein 3D structure. Rather, I have tried as best as possible to summarise my general approach to the problem in a manner that I hope is useful and not too difficult to follow. I apologise in advance for failing to include various references, WWW sites, etc. I...
Lukas
Educational web pages
0
08-30-2008 01:38 AM
Prediction of protein stability after mutation
If you want to make a mutation in your protein to make it behave better in NMR tube, you may consider predicting the change of protein stability and function upon the mutation...it may help to prevent months of wasted time.
Check these web servers: StabilityI-Mutant 2.0
Fold-X
PoPMuSiC
MUpro
Function general
PolyPhen
SPINUS-WEB: Prediction of NMR spectra
Linear Mode
