Dear Pipers, Dr. Shen Yang of the Bax group, who likes to enhance things, has recently made an improved version of his SPARTA system for predicting protein
[Question from NMRWiki Q&A forum] Should manipulate PDB file for SPARTA as an input/pred.tab as an input for nmrPipe?
Should manipulate PDB file for SPARTA as an input/pred.tab as an input for nmrPipe?
HELLO,I have a PDB file of two chains A and B, but as it mentioned in the manual of SPARTA, it read only one chain and the second chain will be ignored. I tried it and it did so. The PDB file I have was the output from Modeling of chain A (that had a mutation). I had refined the modeled structure after docking it into chain B (native). After refinement I have a PDB file of two chains. Now, I have two solutions in mind to get chemical shift prediction plotted in a spectra but I do not know if any of these...
nmrlearner
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11-19-2010 06:28 PM
[Question from NMRWiki Q&A forum] How to plot chemical shift predictions obtained form SPARTA?
How to plot chemical shift predictions obtained form SPARTA?
Dear friends,
I had a mutation in my protein and now I have some amino acids around mutation remained unassigned. To get a way to find the missing peaks I modelled the mutated protein with modeller and out of the pdb file I got the chemical shift predictions using SPARTA. Now that I have chemical shift predictions I want to plot them like a spectra and overlay them to my real spectra to see if it will help me to assign some of the missing peaks. I know for solid-state NMR there is a software, but what about solution NMR?
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nmrlearner
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11-18-2010 06:16 PM
SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of
Abstract NMR chemical shifts provide important local structural information for proteins and are key in recently described protein structure generation protocols. We describe a new chemical shift prediction program, SPARTA+, which is based on artificial neural networking. The neural network is trained on a large carefully pruned database, containing 580 proteins for which high-resolution X-ray structures and nearly complete backbone and 13Cβ chemical shifts are available. The neural network is trained to establish quantitative relations between chemical shifts and protein structures,...
this ... is ... SPARTA (plus)!
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