Hi Brian,
Thank you very much for your advice and the links! I am sure they
will be very useful to me as check them out on my data.
Sincerely,
Weijun
On 08/24/2009 02:39 AM, Brian Smith wrote:
> On Sun, 23 Aug 2009, weijun huang wrote:
>> I am new to NMR, and I wonder what programs I can use to to do
>> backbone assignment of a protein with HNCACB and CBCACONH and N15
>> HSQC spectrums. Any info would be appreciated.
>
> Weijun,
>
> Not sure what you're asking, so here's a catch-all answer.
>
> I'd suggest CcpNmr analysis as a good start. There are tutorials
> describing some of the approaches you can take at:
>
> http://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-software/ccpnmr-analysis/tutorials/protein-assignment
>
> http://www.protein-nmr.org.uk/
> http://www.ccpn.ac.uk/ccpn/software/ccpnmr-analysis/tutorials/ccpnmr-analysis-basics-version-2.0/
>
>
> All these examples use additional/different spectra to the ones you
> have already, but the approach is the same.
>
> Once you have peaks picked and assigned to spin systems via their
> root resonances in analysis, there are several tools you can use to
> assist with backbone assignment. Baerbel has mentioned MARS, and
> analysis also has it's own assignment tool (Automated Backbone
> Sequence under the Assignment item in the main menu bar) which can be
> helpful. There are numerous other automatic methods available (e.g.
> PISTACHIO) and in most cases you can relatively easily export your
> peak information from analysis and get the results back in via the
> formatConverter.
>
> If you are new to NMR, then I would suggest that it is critical
> that you develop your ability to judge whether what any automated
> method tells you is sensible or not, so do follow the principle
> building steps in the tutorial(s) first and have a go with analysis's
> sequential assignment assistant (Link Sequential Spin Systems under
> the Assignment item on the main menu). You will almost certainly need
> to intervene in the assignment yourself in order to resolve
> ambiguities or overlapped peaks.
>
> On a practical matter, then it is likely that you will need
> additional spectra to achieve a complete backbone assignment, unless
> your protein is relatively small and well behaved (and sometimes even
> then). Consider recording carbonyl (HNCO & HNCACO) or proton (e.g.
> HBHACONH & HNHAHB) experiments to supplement your CACB experiments.
>
>
>
> Dr. Brian O. Smith ---------------------- B Smith at bio gla ac uk
> Division of Molecular & Cellular Biology,
> Faculty of Biomedical & Life Sciences,
> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
> Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
> -------------------------------------------------------------------
> The University of Glasgow, charity number SC004401
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