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vmullig / ndm1_design_scripts

Scripts used for Mulligan et al. (2020): Computationally-designed peptide macrocycle inhibitors of New Delhi metallo-beta-lactamase 1
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Residues selection #1

Open almeida85 opened 2 years ago

almeida85 commented 2 years ago

Dear Dr. Mulligan,

I have a question about the script NDM1i_1_design.xml. In the script the pdb 4EXS_Dcys_Lpro.pdb is loaded, where the dipeptide DCys- LPro has residues numbers 301 and 302 respectively. However, in the script, you select residues 237 and 238 and the script still runs. Why is the difference in the numbering?

I am relatively new to Rosetta scripts, and I want to understand the process to apply it to my problem.

Thanks in advance and best regards, Yasser

vmullig commented 2 years ago

Dear Yasser:

In 4EXS_Dcys_Lpro.pdb, residue numbering starts at 42. Internally, Rosetta renumbers residues starting from 1. Since we're adding some additional residues to the stub, it's most convenient to work in Rosetta residue indices, renumbered from 1. On my wishlist for Rosetta improvements are better ways to keep track of residue indices as residues are added or deleted, but for now, one has to do the mental arithmetic.

--Vikram

almeida85 commented 2 years ago

Dear Vikram,

Thank you very much for your reply. I just figured out that by renumbering my peptide after the receptor.

My question is part of a design project I am involved and I am using your work and https://www.nature.com/articles/s41467-021-23609-8 paper as guidelines. I sent you an email early today with a more detailed description of my project. Any help will be very much appreciated.

Regards, --Yasser