Text-based search: First, enter your target name, compound name, ID or SMILES. Then, select which dataset to search.

Structure-based search: First, draw your structure, input SMILES or upload a MOL/SDF file. Then, choose the search type. In the similarity search, the bit vector Morgan fingerprint, an FCFP-like fingerprint, is utilized to characterize the chemical features of a molecule. Finally, select which dataset to search.

The ternary complex structure section displays the PROTAC-mediated ternary complex. For the PROTACs with good degradation capacity but no crystal structures, we also provide the predicted ternary complex models using our PROTAC-Model method (J. Med. Chem. 2021, 64, 21, 16271-16281).

1. Molecule visualization: A 3Dmol.js-enabled visualization window shows the top 10 clusters with no more than 3 representative models per cluster. Action Options: Rotate: Press and hold the left mouse button. Zoom: Use mouse's scroll button. Translate: Press and hold mouse's scroll button.
2. The targeted proteins of PROTACs.
3. Summary of the predicted models. In the Cluster_X_Y.pdb, X and Y represents the best rank from the same cluster and the rank of the model according to the interface energy, respectively. For example, cluster_1_4.pdb belongs to the cluster 1 and is ranked fourth based on the interface energy. PROTAC-Model is used to construct models, which combines the FRODOCK-based protocol and RosettaDock-based refinement. Top 10 clusters with no more than 3 representative models per cluster are displayed online.
4. Statistics of the predicted models. Cluster: The models after clustering. Each cluster contains no more than 3 representative models. All: All models before clustering.

PROTACs based on this warhead or E3 ligand are also displayed on the warhead/E3 ligand page. Taking the warhead page as an example, the features are as follows.

1. The warheads based on same initial structures: The initial structures of warheads might be modified for integration into PROTACs. Thus, this part summarizes these structures to facilitate users to retrieve.
2. The targeted proteins of PROTACs.
3. The E3 ligases of PROTACs (Notice: E3 ligand page doesn't have this filtering option).
4. The list of PROTACs.