Integrating PDBe glycoconjugate information

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Integrating PDBe glycoconjugate information #1459

Open katewarner opened 5 months ago

katewarner commented 5 months ago

Evaluate creating cross-references between GlyGen and Roshan’s covalently linked component (CLC) dataset.

They would like to create cross references from saccharide components in their new CLC dataset to databases like GlyGen (link).
CLC IDs refers to the entire molecule. CCDs are the individual Chemical Components within the CLC, including glycans.
We will discuss how to map to PDBe from GlyGen, then get back to PDBe with a plan

PDBe-GlyGen meeting agenda Discussion slide

ReneRanzinger commented 4 months ago

@katewarner will check what they have on information related to the CLC number

katewarner commented 3 months ago

The CLC data is not yet integrated in the UniChem, however we are in the process, and it will soon will be available in UniChem. We are generating standard InChIs and InChIKeys for the CLCs using RDKit. You can find the complete list of InChIKeys for CLCs here.

Thanks,

Ibrahim Roshan

katewarner commented 2 months ago

I mapped the InChIKeys in the CLC dataset to the InChIKeys in GlyGen, and found that there are 276 glycans in the PDBe CLC dataset