qca-dataset-submission

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Potential dataset: PDB Ligand Expo (30K molecules)

2

The [PDB Ligand Expo](http://ligand-expo.rcsb.org/) contains ~30K small molecules that appear in the PDB. This would be a good set to ensure we have adequate coverage of chemical space, since these...

jchodera

Potential dataset: Molecules from pharma partners in BindingDB

1

[BindingDB](https://www.bindingdb.org/bind/ByPatent.jsp) contains a way to query molecule sets via patents the data was curated from, with a field populated with the name of the filing organization: https://www.bindingdb.org/bind/ByPatent.jsp If we can...

jchodera

Migrate Roche fragment set torsion drive input scripts here

1

We should migrate the Roche fragment set torsion drive input scripts here from wherever they are.

jchodera

Here's some chemistry covered by MMFF94 and GAFF/GAFF2 which we do not currently cover, and which is not currently represented in our datasets: - `[#8]~[#35]`: O-Br single bonds are present...

davidlmobley

We should fall back to the RDKit conformer generator (specifically, ETKDG), the experimental torsion knowledge database) in cases where Omega fails in generating initial conformers for torsion drives and valence...

jchodera

Fix Error Jobs in "OpenFF Group1 Torsions" TorsionDriveDataset

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The "OpenFF Group1 Torsions" dataset was submitted a while ago. There were some error jobs caused by difficulties in full 360 torsion scans. @dgasmith and I tried to fix the...

yudongqiu

[This link](https://disco.chemaxon.com/products/madfast/latest/doc/prepare-molecules.html) has a number of good (but large) open molecule datasets we might consider in the future.

jchodera

Potential dataset: SureChEMBL

2

[SureChEMBL](https://www.surechembl.org) covers the space of patented molecules from our pharma partners. It looks like SureChEMBL can be downloaded in SDF or SMILES form: https://disco.chemaxon.com/products/madfast/latest/doc/prepare-molecules.html#tocid-10 The data lives here: ftp://ftp.ebi.ac.uk/pub/databases/chembl/SureChEMBL/data/

jchodera

This issue is to keep track of chemistries that break common workflows, what their failures are, and if they were resolved. ## Segfaults #### Failure at `oequacpac.OEEnumerateFormalCharges()` (used to expand...

ChayaSt

MlPepper RECAP Fragments v1.0

3

The MLPepper RECP fragment dataset for ML partial charge training, see the readme for more details. ## New Submission Checklist - [x] Created a new folder in the submissions directory...

jthorton