Re: Protein Sequence format I-PINE webserver

[Lee, Woonghee]

Dear Arun,

 

If you are using NMRFAM-SPARKY, you can easily renumber by two-letter-code “rn”. I-PINE is designed to use 1 as the first sequence and you have to use G1 as default. However, there is workaround like you can purposely omit signals from the tag in the input files for the I-PINE web server and use native sequence numbers.

 

Best,

Woonghee

 

--

Woonghee Lee, I.E.I.P., M.S., Ph.D.

 

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Department of Chemistry

University of Colorado Denver

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From: Arun Gupta <arung...@gmail.com>
Date: Monday, November 2, 2020 at 6:29 AM
To: Woonghee Lee <wh...@nmrfam.wisc.edu>
Subject: Protein Sequence format I-PINE webserver

 

Dear Woonghee

 

What should be  the  protein sequence format for submission on I-PINE webserver which includes the extra N-terminal residues which are coming of  tag cleavage & starting translation residue methionine.For e.g GSHM. Although, these extra N-terminal residues are important for the correct & complete assignment of the protein. But I want the assignment to start from the 1st residue of the main chain of protein sequence e.g  in my case, Asp1 /D1 instead of  G1/ Gly1 to ease the BMRB submission at later stage. 

 

I mostly prefer to  submit the assignment jobs on I-PINE web server and it has worked pretty well for me. 

 

Thanks &  Regards

 

Arun

 

--

Arun Gupta PhD, MRSC

Research Fellow

Chemistry Department

University of Warwick
Gibbet Hill Road
Coventry CV4 7AL
United Kingdom