Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Create sugar or carbohydrate selection using GLYCAM nomenclature #4563

Open
hmacdope opened this issue Apr 12, 2024 · 1 comment · May be fixed by #4790
Open

Create sugar or carbohydrate selection using GLYCAM nomenclature #4563

hmacdope opened this issue Apr 12, 2024 · 1 comment · May be fixed by #4790

Comments

@hmacdope
Copy link
Member

hmacdope commented Apr 12, 2024

From @orbeckst in #4562

Btw, I couldn't access the GLYCAM nomenclature link but I found it in the internet archive (http://web.archive.org/web/20230330152511/https://glycam.org/docs/forcefield/glycam-naming-2/index.html). It would be an interesting project to collect all GLYCAM residue names so that we can create a selector "sugar" (or "carbohydrate") that selects anything with those residue names (similar to how "protein" selects anything that has the 20+ amino acid residue names).

@talagayev
Copy link
Member

@hmacdope I had a quick look now into it to see if there are good websites, where the whole nomenclature is located and also found mainly the full nomenclature on the glycam website itself, with it also containing the PDB/CHARMM nomenclature for the sugars :

https://glycam.org/docs/othertoolsservice/2016/06/09/3d-snfg-list-of-residue-names/index.html

Here is the second location where I found a collection of all of the glycam abbreviations:

https://github.com/pablo-arantes/making-it-rain/blob/main/Glycam.ipynb

I guess it would be then also good to have in the same direction to have also a water selector, but here I don't know any resource that would have all of the water abbreviations collected in one place, so it would be possibly more checking/researching required, especially if we want to cover some less common water abbreviations.

@talagayev talagayev linked a pull request Nov 14, 2024 that will close this issue
5 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

Successfully merging a pull request may close this issue.

2 participants