ROC-AUC scores and average precision scores for RF and GBT classification models with 8 features.

(a) ROC-AUC score. Green line represents the standard deviation for ROC-AUC score. (b) Average precision score.</p

ROC-AUC curve, false positive rate-threshold curve and precision-recall curve for ten ESM RF models.

a) ROC-AUC curve. b) False positive rate-threahold curve. c) Precision-recall curve.</p

Protein kinase tree based on the key-position only MSA and structural mapping of the key positions for FAK and BRD4.

In (b) and (c), cyan represents the structure of CRBN; purple represents the structure of FAK and BRD4; yellow balls and sticks represent PROTACs for FAK and BRD4; green balls and sticks represent the predicted key positions.</p

Interactions between predicted PROTACs and the CRBN-target protein complex structures.

(a) Ligand-target interactions between the PROTAC and the complex structure for P12757. (b) 2D ligand-target interactions between the PROTAC and the complex structure for P12757. A and B represent the chain ID for P12757 and CRBN, respectively. (c) Ligand-target interactions between the PROTAC and the complex structure for Q9UER7. (d) 2D ligand-target interactions between the PROTAC and the complex structure for Q9UER7. B and C represent the chain ID for CRBN and Q9UER7, respectively. (e) Ligand-target interactions between the PROTAC and the complex structure for Q9H1I8. (f) 2D ligand-target interactions between the PROTAC and the complex structure for Q9H1I8. A and B represent the chain ID for Q9H1I8 and CRBN, respectively. Cyan sticks represent interacting residues on CRBN and green sticks represent interacting residues on the target protein. Yellow balls and sticks represent the ligand structure. Color representations for interaction types are shown in the figure legend.</p

ROC-AUC, false positive rate-threshold, precision-recall curves for RF (left panel) and GBT (right panel) models on the external test set in which the negative samples are not in the sample folds with the positive samples.

(a) ROC-AUC curve for the RF model. (b) ROC-AUC curve for the GBT model. (c) false positive rate-threshold curve for the RF model. (d) false positive rate-threshold curve for the GBT model. (e) precision-recall curve for the RF model. (f) precision-recall curve for the GBT model. AUC represents the average ROC-AUC score, AP represents the average precision score.</p

Structural mapping of the key positions for P12757, Q9UER7 and Q9H1I8.

Purple colors represent CRBN and the target protein, respectively. Yellow and green balls and sticks represent predicted PROTACs and the top ranked positions, respectively. H and B represent α helix and β sheet, respectively.</p

Supporting information for methods and results.

Supplemental materials for PrePROTAC model training, testing and prediction. Additional results for eSHAP analysis on the human protein kinases. (PDF)</p

Interactions between predicted PROTACs and the CRBN-target protein complex structures.

(a) Ligand-target Interactions between CRBN and its crystallized ligand LVY in 4TZ4. (b) 2D Ligand-target Interactions between CRBN and its crystallized ligand LVY in 4TZ4. C represents the PDB chain ID for CRBN. (c) Ligand-target interactions between PROTAC3269 and the complex structure of P12757 and CRBN. (d) 2D Ligand-target interactions between PROTAC3269 and the complex structure of P12757 and CRBN. A represents the chain ID for the target protein. B represents the chain ID for CRBN. (e) Ligand-target interactions between PROTAC3055 and the complex structure of Q9UER7 and CRBN. (f) 2D Ligand-target interactions between PROTAC3055 and the complex structure of Q9UER7 and CRBN. C represents the chain ID for the target protein. B represents the chain ID for CRBN. (g) Ligand-target interactions between PROTAC2145 and the complex structure of Q9H1I8 and CRBN. (h) 2D Ligand-target interactions between PROTAC2145 and the complex structure of Q9H1I8 and CRBN. A represents the chain ID for the target protein. B represents the chain ID for CRBN. Cyan and green sticks represent interacting residues on CRBN and the target protein, respectively. Yellow balls and sticks represent the ligand structures. Color representations for the interaction types are shown in figure legend.</p

Overview of the PrePROTAC model and application process.

Overview of the PrePROTAC model and application process.</p

A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites-5

<p><b>Copyright information:</b></p><p>Taken from "A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites"</p><p>http://www.biomedcentral.com/1471-2105/8/S4/S9</p><p>BMC Bioinformatics 2007;8(Suppl 4):S9-S9.</p><p>Published online 22 May 2007</p><p>PMCID:PMC1892088.</p><p></p>owest). The structures shown in the left and the right columns are holo and apo proteins, respectively. The known ligand binding site is located in the white circle. The RMSD between the holo and apo protein across the whole structure is shown above the arrow. (A) Immunoglobulin 48g7 germline fab (PDB id: 1AJ7 and 2RCS); (B) Adenylate kinase (PDB id: 1AKE and 4AKE); (C) HIV-1 reverse transcriptase (PDB id: 1VRT and 1RTJ); (D) Maltodextrin binding protein (PDB id: 1ANF and 1OMP)