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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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Nwchem mol2 #171

Open nkkchem opened 4 years ago

nkkchem commented 4 years ago

I added the NWChem optimized structures (mol2) of Yeast with partial charges computed with Mulliken population.

samseaver commented 4 years ago

What do you mean by "Yeast"? Do these structures map to any particular set of compound aliases in a published model for yeast? We can map the InChI-Keys to whatever we have, but we'd like to know where these came from.

nkkchem commented 4 years ago

This is the compound list of Yarrowia lipolytica CL1B122  model curated on the pathway genome database.  https://cyc.pnnl.gov/organism-summary?object=YARROWIA

samseaver commented 4 years ago

Can you commit a flat file showing a direct mapping between the names of the mol files you committed and the Cyc identifiers in that database? We've a number of them in our aliases, but because of how different databases are curated with different policies, we get structural conflicts between Cyc identifiers that are supposed to be the same compound. Having the source will be a great help.

samseaver commented 4 years ago

Can you also add a simple README that explains the source of the data with links etc. Thanks