Datasets:
Update README.md
Browse files
README.md
CHANGED
@@ -24,10 +24,6 @@ ProFSADB is a large-scale protein-ligand interaction pretraining dataset generat
|
|
24 |
2. **Pocket Definition**: Excludes the five nearest residues on each fragment side to focus on long-range interactions. Pockets are defined as residues with ≥1 heavy atom within **6Å** of the fragment.
|
25 |
3. **Quality Control**: Complexes are filtered to retain only high-confidence interaction pairs.
|
26 |
|
27 |
-
**Intended Use**
|
28 |
-
- Pretrain pocket encoders for interaction-aware protein representation learning.
|
29 |
-
- Downstream tasks: Pocket druggability prediction, ligand binding affinity prediction, pocket matching, and de novo drug design.
|
30 |
-
|
31 |
**Unique Advantages**
|
32 |
- **Scale**: 50× larger than existing experimental complex datasets (e.g., PDB).
|
33 |
- **Interaction Modeling**: Contrastive pretraining aligns pocket features with pretrained small-molecule representations.
|
@@ -54,4 +50,9 @@ If you use ProFSADB or the ProFSA method, please cite:
|
|
54 |
**Links**
|
55 |
|
56 |
- **Paper**: [Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment](https://openreview.net/forum?id=uMAujpVi9m)
|
57 |
-
- **Homepage**: [Project Page](https://atomlab.yanyanlan.com/project/profsa/)
|
|
|
|
|
|
|
|
|
|
|
|
24 |
2. **Pocket Definition**: Excludes the five nearest residues on each fragment side to focus on long-range interactions. Pockets are defined as residues with ≥1 heavy atom within **6Å** of the fragment.
|
25 |
3. **Quality Control**: Complexes are filtered to retain only high-confidence interaction pairs.
|
26 |
|
|
|
|
|
|
|
|
|
27 |
**Unique Advantages**
|
28 |
- **Scale**: 50× larger than existing experimental complex datasets (e.g., PDB).
|
29 |
- **Interaction Modeling**: Contrastive pretraining aligns pocket features with pretrained small-molecule representations.
|
|
|
50 |
**Links**
|
51 |
|
52 |
- **Paper**: [Self-supervised Pocket Pretraining via Protein Fragment-Surroundings Alignment](https://openreview.net/forum?id=uMAujpVi9m)
|
53 |
+
- **Homepage**: [Project Page](https://atomlab.yanyanlan.com/project/profsa/)
|
54 |
+
|
55 |
+
|
56 |
+
# ProFSA Model Weights
|
57 |
+
|
58 |
+
The weights of our best model pretrained using the ProFSADB data is located at `checkpoint_best.pt`.
|