POKY for Non-Ribosomal Cyclic Peptide 3D-Structure Calculation

[Thinh Bui]

Dear Prof. Lee,

I am working on the NMR-based structure elucidation of a non-ribosomal cyclic peptide (~1500 Da) containing unusual (non-proteinogenic) amino acid residues and covalent crosslinks. I would like to ask whether POKY can be used for the analysis and 3D structure calculation of such systems.

Specifically, is POKY applicable non-proteinogenic amino acids, and if so, does the general workflow (assignment, NOE extraction, and export to Xplor-NIH) remain the same as for proteins, or are special modifications required?

Thank you very much for your time and guidance.

Best,
Thinh

[Lee, Woonghee]

Hi,

Certainly, you can use POKY for that by hybrid approach combining automation tools and manual interventions. At the structure calculation stage, do a few automation steps to gather restraints first, then you can use Xplor-NIH for the final touch.

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

Assistant Professor & Data Science and Chemistry Certificate Program Director
Department of Chemistry

Center for Advanced Computational Molecular Science
University of Colorado Denver
1151 Arapahoe St. (Science Bldg.) Rm 4128A (office), Rm 4128 (dry lab), Rm 4133 (wet lab)
Denver, CO 80217-3364, USA
Office: +1-303-315-7672

woongh...@ucdenver.edu

https://poky.clas.ucdenver.edu
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https://clas.ucdenver.edu/chemistry/woonghee-lee
https://clas.ucdenver.edu/chemistry/data-science-and-chemistry-certificate

Shipping/Mailing Address:
Woonghee Lee
1201 5th St. UCD CHEM-194
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From: nmr-s...@googlegroups.com <nmr-s...@googlegroups.com> on behalf of Thinh Bui <tienth...@gmail.com>
Sent: Monday, January 26, 2026 5:42:59 AM
To: NMR POKY/SPARKY USER GROUP <nmr-s...@googlegroups.com>
Subject: [NMR POKY/SPARKY] POKY for Non-Ribosomal Cyclic Peptide 3D-Structure Calculation

 

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