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Oligosaccharide detection in BioIn #6

Open LobeliaG opened 2 years ago

LobeliaG commented 2 years ago

Currently BioIn detects only the ligands associated with the PDB structures. Although it does not apparently affect the protein processing, many structures have a number of oligosaccharide molecules attached to them which go undetected in our software. It might be better if we could detect and subsequently clean them particularly as well for a more refined version. PDB used here- 7ZJ7

website carbissue carb issue1 carb issue2

SumedhaBhosale commented 2 years ago

PDB ID = 2D44. contains oligosaccharides. BioIn cannot detect and process such proteins !

SumedhaBhosale commented 2 years ago

PDB ID = 3J0A - contains oligosaccharides. BioIn cannot detect and process this !

LobeliaG commented 2 years ago

For structures with lipid molecules associated with them, the lipids are generally listed under the ligand category in the database. Thus, our software is able to detect and show then under ligand report and can ultimately clean them in Str. editor. So the software picks up only the data that is listed as ligands in RCSB site, and not the other categories. Here is one example. Detectable molecules The full data for this structure can be found at https://www.rcsb.org/structure/4RET