Is there a way to generate IdoA2S in 1C4 conformation instead of 4C1?

[jsdumalaog]

Whenever I generate IdoA/IdoA2S residues using GAG-Builder, I always get IdoA2S in 4C1 conformation. Is there a way to directly obtain 1C4 conformation? Thanks.

[Lachele]

Theoretically, you can use the Build Via Text option (https://glycam.org/txt/), but I can only get LIdopA in 1C4. Adding the 2S gives a 400 (InvalidInputPayload).

If you put the following into the condensed sequence box at the /txt/ site, you will get a molecule.

LIdopA(1C4)a1-OH

But I can't have 1C4 and 2S present in the sequence at the same time.

I don't remember the proper way to string them together, but neither of these works:

LIdopA(1C4)[2S]a1-OH     ## these currently
LIdopA[2S](1C4)a1-OH     ## do not work

@gitoliver or @vraid - is this a code thing? Am I being fuzz-brained about the nomenclature?

Anyway, you can get LIdopA in 1C4 now, but not LIdopA[2S]. To do that, copy the sequence into the build-via-txt box and add the '(1C4)' to each LIdopA as shown above.

[gitoliver]

Substituted versions of these prep files were not generated originally, and I guess I must have skipped this with my code that generates all possible substitutions... Maybe because they don't follow the GLYCAM residue naming convention.

Anyway yes we don't support this.

[Lachele]

There are established procedures for adding sulfate as a derivative. It can be added to the LIdopA(1C4) structure according to the instructions at the link below. We already do this sort of addition in the Sequence builder, so I think it might merely be a matter of giving the parser the instructions needed to parse the information. Of course, given the electronic characteristics of LIdopA, the simple methods below might not be optimal, but they will provide something to test.

If we do not already have a preference in place, I recommend that the ring pucker come first so that the information that directly affects the largest part of the structure is first. That should also ease parsing where the pucker requires a special geometry template (prep file).

https://glycam.org/docs/help/2014/04/04/adding-chemical-derivatives-to-glycam-residues/index.html