Update README.md
Browse files
README.md
CHANGED
|
@@ -11,16 +11,16 @@ tags:
|
|
| 11 |
|
| 12 |
# PXR Challenge Multi-method Cofolding
|
| 13 |
|
| 14 |
-
This dataset contains
|
| 15 |
Ligands are derived from the OpenADMET PXR Challenge and contain known binders, known agonists, and inactives. More on the ligand set can be found here: https://huggingface.co/spaces/openadmet/pxr-challenge
|
| 16 |
|
| 17 |
-
Each
|
| 18 |
|
| 19 |
Deposited is the raw cofolding output with all confidence predictions and other data files.
|
| 20 |
|
| 21 |
### Contents:
|
| 22 |
- `input_data`: raw SMILES tables, PDB64 rerefined input structures, hPXR LBD sequence, and ColabFold MSA used for all cofolding runs.
|
| 23 |
-
- `pdb64`: cofolding predictions for a 70-system rerefined PXR crystal set. Untemplated and templated with the protein
|
| 24 |
- `structure_challenge`: cofolding predictions and inputs for 184 structure-challenge ligands.
|
| 25 |
- `activity_challenge`: cofolding predictions for 513 activity-challenge ligands.
|
| 26 |
|
|
|
|
| 11 |
|
| 12 |
# PXR Challenge Multi-method Cofolding
|
| 13 |
|
| 14 |
+
This dataset contains >40,000 cofolding predictions using three different methods (OpenFold3, Boltz2, Chai1) for the nuclear hormone receptor hPXR and with >600 ligands.
|
| 15 |
Ligands are derived from the OpenADMET PXR Challenge and contain known binders, known agonists, and inactives. More on the ligand set can be found here: https://huggingface.co/spaces/openadmet/pxr-challenge
|
| 16 |
|
| 17 |
+
Each cofolding method was run using default settings and untemplated, except where noted. Each protein/ligand/method/parameter set generated 20-25 structures (5 samples * 4 or 5 random seeds)
|
| 18 |
|
| 19 |
Deposited is the raw cofolding output with all confidence predictions and other data files.
|
| 20 |
|
| 21 |
### Contents:
|
| 22 |
- `input_data`: raw SMILES tables, PDB64 rerefined input structures, hPXR LBD sequence, and ColabFold MSA used for all cofolding runs.
|
| 23 |
+
- `pdb64`: cofolding predictions for a 70-system rerefined PXR crystal set. Untemplated and templated with the protein crystal coordinates.
|
| 24 |
- `structure_challenge`: cofolding predictions and inputs for 184 structure-challenge ligands.
|
| 25 |
- `activity_challenge`: cofolding predictions for 513 activity-challenge ligands.
|
| 26 |
|