Files and READMEs cleanup

.gitignore

@@ -168,4 +168,5 @@ data/PROTAC-Pedia.csv
 data/cellosaurus.txt
 logs/
 notebooks/per-protein*
-*slurm*.out
+*slurm*.out
+.DS_Store

README.md

@@ -98,6 +98,10 @@ If you use this tool in your research, please cite the following paper:
 }
 ```
 
+The directories [logs](logs/) and [reports](reports/) contain the logs and reports generated during the experiments reported in the paper. Additionally, in [reports](reports/), one can find the pickled Optuna studies for the reported experiments.
+
+The directory [models](models/) contains the trained models for the experiments reported in the paper.
+
 ## 📜 License
 
 This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.

data/README.md

@@ -1,4 +1,9 @@
 # Data
 
-* [PROTAC-DB](http://cadd.zju.edu.cn/protacdb/about)
-* [PROTAC-Pedia](https://protacpedia.weizmann.ac.il/ptcb/main)
+- [PROTAC-DB](http://cadd.zju.edu.cn/protacdb/about)
+- [PROTAC-Pedia](https://protacpedia.weizmann.ac.il/ptcb/main)
+- [Curated dataset](PROTAC-Degradation-DB.csv)
+
+The folder [studies](studies/) contains the data used in each study reported in our paper.
+
+The folder [processed](processed/) contains pickled dictionary files used for standardize cell names and to map Uniprot IDs to their amino acid sequences.

data/processed/multiple_cell_types.csv

@@ -1,121 +0,0 @@
-Compound ID,Cell Type,Comments,DC50 (nM),Dmax (%)
-106,"RS4;11, MOLM-13","Direct degration studies in this paper only conducted for first and final compounds; during the med chem campaign cell viability was used as the read out. Complex structure with the ligand was modeled based on 4Z93. IC50 of the ligand is between 2nM and 7nM, depending on which BRD. DC50 is between 3nM-10nM.",< 10 nM,100 %
-107,"RS4;11, MOLM-13","Complex structure with the ligand was modeled based on 4Z93. IC50 of the ligand is between 2nM and 7nM, depending on which BRD",< 1 nM,100 %
-108,"RS4;11, MOLM-13","Complex structure with the ligand was modeled based on 4Z93. IC50 of the ligand is between 2nM and 7nM, depending on which BRD",< 1 nM,100 %
-109,"RS4;11, MOLM-13","Complex structure with the ligand was modeled based on 4Z93. IC50 of the ligand is between 2nM and 7nM, depending on which BRD",~ 3 nM,
-110,"RS4;11, MOLM-13","Complex structure with the ligand was modeled based on 4Z93. IC50 of the ligand is between 2nM and 7nM, depending on which BRD",~ 10 nM,
-111,"MV4-11, MOLM-13, KG1","They show ""dual"" degradation but don't do any test that the dual degradation actually made any difference. They make it sound novel but of course we can call our PROTACs ""dual"" degraders if you can the off-targets ""targets"". EC50 of ligand is in measured in MV4-11 cell line. EC50 of PROTAC is between 4.5nM-6.94nM (depended on the cell line).",< 5 nM,~ 100 %
-149,"MOLT-4, MOLM14","General kinase PROTAC, DCmax is for the most degraded kinase. IC50 of the ligand is for 193 kinases in the panel. IC50 of the PROTAC is by FLT3 kinase activity.",< 100 nM,> 85 %
-150,"MOLM14, MV4-11",IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines,,
-151,"MOLM14, MV4-11",IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines,,
-152,"MOLM14, MV4-11",IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines,,
-153,"MOLM14, MV4-11",IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines,,
-154,"MOLM14, MV4-11",IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines,,
-155,"MOLM14, MV4-11",IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines,,
-156,"MOLM14, MV4-11",IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines,,
-157,"MOLM14, MV4-11",Dmax is difficult to quantify because AC220 raises FLT3 expression levels. IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines. EC50 of PROTAC was measured on MOLM-14 cell lines.,< 10 nM,~ 100 %
-158,"MOLM14, MV4-11",Dmax is difficult to quantify because AC220 raises FLT3 expression levels. IC50 of ligand is 1.6 nM (binding); 1.1-4 (activity). EC50 of ligand is measured on MOLM-14 cell lines. EC50 of PROTAC was measured on MOLM-14 cell lines.,< 10 nM,~ 100 %
-159,"MOLM14, MV4-11",IC50 of ligand is inhibitory - data from Selleckchem. EC50 of the lidand is Src-dependent cell proliferation - data from Selleckchem.,~ 100 nM,~ 50 %
-202,"NAMALWA, XLA","DC50 is 9.1 nM (WT BTK, NAMALWA cells), 14.6 nM (WT BTK, XLA cells), 14.9 nM (C481S, XLA cells). IC50 of PROTAC is 46.9 (WT BTK), 20.9 (C481S). IC50 of ligand is 51.0 nM (WT BTK), 30.7 (C481S)",< 14.9 nM,> 99 %
-258,"MV-4-11 SK-MEL-5, NCI-H1568","EC50 of PROTAC is 28nM in MV-4-11, 68nM in NCI-H1568. DC50 is (SMARCA2 6nM, SMARCA4 11nM, PBRM1 32nM in MV-4-11; SMARCA2 3.3nM, PBRM1 15.6nM in NCI-H1568)",< 32 nM,
-283,"HeLa, DLBCL",DC50 value is for HeLa cells. DC50 is 0.61 uM for DLBCL cells. DMAX value is for HeLa cells. DMAX is 96 % for DLBCL cells.,0.79 uM,92 %
-290,Jurkat and Panc Tu‐I,"proteomics of PDEdelta degradation show upregulation of enzymes involved in lipid metabolism - deltasonamide 1 also causes this. Dmax was measured in Panc-Tu-1 cell line. DC50 is 83.4% (24 h, Panc-Tu-1), 85% (24 h, 1 uM, Jurkat). IC50 Deltasonamide 1 is 203 pM, and of the Bn derivative is 8 nM.",48 nM,> 83.4 %
-291,Jurkat and Panc Tu‐I,"proteomics of PDEdelta degradation show upregulation of enzymes involved in lipid metabolism - deltasonamide 1 also causes this. IC50 Deltasonamide 1 is 203 pM, and of the Bn derivative is 8 nM.",,
-323,"HeLa, MV4;11, A549",DC50 is 1-3nM,< 3 nM,100 %
-324,"HeLa, MV4;11, A549",DC50 is 10-30nM,< 30 nM,99 %
-327,SU-DHL-1 and NCI-H2228,"competition with ligand only slightly rescued protein degradation. EC50 of ligand and PROTAC is measured on SUDHL-1 cell line. DC50 is SU-DHL-1: 3 ± 1 nM, NCI-H2228: 34 ± 9 nM.",< 34 nM,> 90 %
-328,SU-DHL-1 and NCI-H2228,"competition with ligand only slightly rescued protein degradation. EC50 of ligand and PROTAC is measured on SUDHL-1 cell line. DC50 is SU-DHL-1: 11 ± 2 nM, NCI-H2228: 59 ± 16 nM.",< 59 nM,> 90 %
-331,"MCF-7, MM.1S",DC50 and Dmax are for MCF-7 cells,34 nM,70.5 %
-343,DU145/Cy,"Tested reversal of docetaxel resistance by degradation of CYP, followed by lysis and WB, model with the ligand is available in previous publication",,
-344,DU145/Cy,"Tested reversal of docetaxel resistance by degradation of CYP, followed by lysis and WB, model with the ligand is available in previous publication",,
-345,DU145/Cy,"Tested reversal of docetaxel resistance by degradation of CYP, followed by lysis and WB, model with the ligand is available in previous publication",,
-346,DU145/Cy,"Tested reversal of docetaxel resistance by degradation of CYP, followed by lysis and WB, model with the ligand is available in previous publication",,
-375,"Namalwa, CA-46, Ramos","tested also biological effects - proliferation and caspase activity on BL cells. IC50 of ligand is 14 nM (BD1), 3.5 nM (BD2). IC50 of PROTAC is 90 nM (BD1), 28 nM (BD2).",< 1 nM,~ 100 %
-376,"HBL1, Ramos, Mino, IgE MM","also degrades ibrutinib-resistant C481S BTK. DC50 is 6.3 nM (HBL1), 8.5 nM (Ramos), 9.2 nM (Mino), 11.4 nM (IgE MM)",< 11.4 nM,94 %
-388,"Ramos, THP-1",Ligand name is from PMID 24068666,,
-389,"Ramos, THP-1",Ligand name is from PMID 24068666,,
-390,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 18-33%,,< 33 %
-391,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 15-34%,,< 34 %
-392,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 36-64%. DC50 is 1487 - 1994.5 nM.,< 1994.5 nM,< 64 %
-393,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 68-85%. DC50 is 36.9 - 398.5 nM.,< 398.5 nM,> 68 %
-394,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 63-84%. DC50 is 21.8 - 469.9 nM.,< 469.9 nM,> 63 %
-395,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 75-87%. DC50 is 4.5 - 90.5 nM.,< 90.5 nM,> 75 %
-396,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 71-85%. DC50 is 5.9 - 217.7 nM.,< 217.7 nM,> 71 %
-397,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 80-87%. DC50 is 1.1 - 37.4 nM.,< 37.4 nM,> 80 %
-398,"Ramos, THP-1",Ligand name is from PMID 24068666. DCmax is 70-85%. DC50 is 9.7 - 184.1 nM.,< 184.1 nM,> 70 %
-399,"Ramos, THP-1",Ligand name is from PMID 24068666,,
-400,"Ramos, THP-1",Ligand name is from PMID 24068666,,
-467,"MV4-11, MOLM-14","IC50 of ligand is FLT-3 ITD 10.3± 0.3nM, FLT-3 WT 7.4± 0.3nM. IC50 of PROTAC is FLT-3 ITD 43± 3.2nM, FLT-3 WT 36± 3nM.",,
-472,"MDA-MB-231, HeLa",DC50 error ± 1.0 nM. DMAX error ± 1.1 %.,9.5 nM,99.6 %
-473,"MDA-MB-231, HeLa",DC50 error ± 81.3 nM. DMAX error ± 10.1 %.,45.9 nM,34.5 %
-561,"MCF-7, MDA-MB-231, HepG2, LO2, B16",Dmax is measured in 10uM. EC50 of PROTAC is MCF-7: 2.70 ± 0.19 MDA-MB-231: 21.21 ± 1.95 HepG2: 18.70 ± 1.65 LO2: 41.11 ± 3.70 B16: 22.68 ± 2.03 uM. EC50 of ligand is MCF-7: 4.17 ± 0.31 MDA-MB-231: 21.33 ± 1.96 HepG2: 10.59 ± 0.94 LO2: 35.57 ± 2.81 B16: 14.49 ± 1.28 uM.,~ 0.5 uM,81 %
-562,"Karpas 422,ULA, SUDHL4, OCI-Ly1, Ramos","half the paper develops the ligand and checks its selectivity. Dmax is 76% Karpas 422, 59% ULA, 84% SUDHL4, 82% OCI-Ly1, 82% Ramos.",~ 1 uM,> 76 %
-572,"SR, H2228, NCI–H69, NCI–H1688, NCI–H446","EC50 of ligand is 2.7 ± 0.4nM (SF cells), 58.2 ± 20.7 nM (H2228 cells). EC50 of PROTAC is 1.7 ± 1 nM (SF cells), 46nM ± 16 nM (H2228 cells).",7.0 nM,
-573,"OVCAR8 (WT EGFR), HeLa (EGFR Exon 20 Ins), SKBr3 (HER2)",DC50 is for WT EGFR. DC50 for EGFR Exon 20 Ins is 736.2 nM. DMAX is for WT EGFR. DMAX for EGFR Exon 20 Ins is 68.8 %.,39.2 nM,97.6 %
-574,"HCC827 (Exon 19 del), H3255 (L858R)",DC50 is for EGFR (Exon 19 del). DC50 for EGFR (L858R) 22.3 nM. DMAX is for EGFR (Exon 19 del). DMAX for EGFR (L858R) 96.6 %.,11.7 nM,98.9 %
-578,"RS4;11, MV4;11, MOLM-13,",EC50 of ligand is 55.8-207 nM.,,
-579,"RS4;11, MV4;11, MOLM-13,",EC50 of PROTAC is 19.7nM-311nM. EC50 of ligand is 55.8-207 nM.,,
-580,"RS4;11, MV4;11, MOLM-13,",EC50 of PROTAC is 0.379nM-2.23nM. EC50 of ligand is 55.8-207 nM.,,
-581,"RS4;11, MV4;11, MOLM-13,",EC50 of PROTAC is 0.038nM-0.56nM. EC50 of ligand is 55.8-207 nM.,,
-582,"RS4;11, MV4;11, MOLM-13,",EC50 of PROTAC is 0.02nM-0.19nM. EC50 of ligand is 55.8-207 nM.,,
-583,"RS4;11, MV4;11, MOLM-13,",EC50 of PROTAC is 0.02nM-0.19nM. EC50 of ligand is 55.8-207 nM.,,
-584,"RS4;11, MV4;11, MOLM-13,",EC50 of PROTAC is 0.0083nM-0.062nM. EC50 of ligand is 55.8-207 nM.,< 0.5 nM,100 %
-589,"MCF-7, U2OS, MDA-MB-231, MDA-MB-435, Flag-Cdc20, MDA-MB-231, 22Rv1, LNCaP",EC50 of PROTAC is 2.6 uM for MDA-MB-231 and 1.99 uM for MDA-MB-435,1.6 uM,
-607,"Hella, RI-1, EOL-1, A-204",DC50 is 1.76 nM and 4.5 nM,< 4.5 nM,90 %
-630,"Molm-16, SU-DHL-1",EC50 of PROTAC is 10nM-35nM,0.06 uM,
-661,"RS4;11, MV4;11",EC50 of ligand and PROTAC was measured in RS4;11 cell line.,,98 %
-662,"RS4;11, MV4;11",EC50 of ligand and PROTAC was measured in RS4;11 cell line.,,99 %
-692,"LNCaP, VCaP, and 22Rv","DC50 is 0.86nM in LNCaP, 0.76 in VCaP and 10.4 nM at 1uM in 22Rv1. EC50 in cells is 0.25nM for LNCaP, 0.34 nM for VCaP, 183nM for 22Rv1.",< 10.4 nM,> 95 %
-727,"MV4-11, Molm-13","EC50 of ligand is 0.370 uM for MV4- 11, 3.369 uM for Molm-13. EC50 of PROTAC is 1.648uM for MV4-11, >10uM for Molm-13",,
-728,"MV4-11, Molm-13","EC50 of ligand is 0.370 uM for MV4- 11, 3.369 uM for Molm-13. EC50 of PROTAC is 0.025uM for MV4-11, 0.18uM for Molm-13",,
-730,"MV4-11, Molm-13","EC50 of ligand is 0.370 uM for MV4- 11, 3.369 uM for Molm-13. EC50 of PROTAC is 0.032uM for MV4-11, 0.177uM for Molm-13.",,
-731,"MV4-11, Molm-13","EC50 of ligand is 0.370 uM for MV4- 11, 3.369 uM for Molm-13. EC50 of PROTAC is 3.429uM for MV4-11, >10uM for Molm-13.",,
-779,HOP62/INC-H23,Inactive PROTAC for KRAS based on AMG-510.,,
-814,E14 mouse embryonic stem cells; Human colon cancer cell line HCT116,"For HDAC1/HDAC2/HDAC3, the Dmax of this PROTAC is: >85%, >76%, >63%, respectively.",~ 1 uM,
-815,Pancreatic cancer cell lines BxPC-3; MIA PaCa-2,"XD2-149 was initially designed to degrade STAT3. However, experiments showed that XD2-149 down-regulate STAT3 level in a proteasome-independent manner. Proteomics data revealed that an E3 ligase, ZFP91, was the true substrate for this PROTAC. This paper reported a total of 22 PROTACs, which differed from each other in linker design and E3 binder choices (pomalidomide/thalidomide/lenalidomide). However, the authors didn't mention whether the remaining 21 molecules could degrade ZFP91 or not. It is also interesting that pomalidomide itself can induce the degradation of CRBN neo-substrates like ZFP91 (DC50: 0.42uM, 5-fold less potent than XD2-149), since pomalidomide can remodel CRBN surface for binding proteins like ZFP91 (Nat Med., 2019, doi: 10.1038/s41591-019-0668-z).",~ 70 nM,> 90 %
-830,KYSE520 esophageal cancer cell line; MV4;11 cell line,Degradation rate for KYSE520 cell: 87% (1uM compound); Degradation rate for MV4;11 cell: 85% (0.1uM compound),,
-832,KYSE520 esophageal cancer cell line; MV4;11 cell line,Dmax for KYSE520 cell: >95%; Degradation rate in MV4;11 cell: 47% (0.1uM compound),,
-833,KYSE520 esophageal cancer cell line; MV4;11 cell line,Dmax for KYSE520 cell: >95%; Degradation rate in MV4;11 cell: 6% (0.1uM compound),,
-834,KYSE520 esophageal cancer cell line; MV4;11 cell line,Degradation rate in KYSE520 cell: 90% (1uM compound); Degradation rate in MV4;11 cell: 8% (0.1uM compound),,
-835,KYSE520 esophageal cancer cell line; MV4;11 cell line,DC50 for KYSE520 cell: 6.0nM;DC50 for MV4;11 cell: 2.6nM; EC50 for KYSE520 cell: 0.66uM; EC50 for MV4;11 cell: 9.9nM;,6.0 nM,100 %
-837,KYSE520 esophageal cancer cell line; MV4;11 cell line,Dmax for KYSE520 cell: >95%; Dmax for MV4;11 cell: >90%,,> 95 %
-838,KYSE520 esophageal cancer cell line; MV4;11 cell line,Dmax for KYSE520 cell: >80%; Degradation rate for MV4;11 cell: 9% (0.1uM compound),,
-839,"HeLa, HL60, MV4;11","pEC50 for MV4;11 and HL60 cells: 6.75±0.03 and 5.84±0.06, respectively.
-pDC50 for Brd4 short/Brd4 long/Brd3/Brd2: 7.0/7.0/6.5/6.2, respectively (24h, HeLa cells).
-Dmax for Brd4 short/Brd4 long/Brd3/Brd2: 96%/97%/97%/93%, respectively (HeLa cells).",< 0.1 uM,> 93 %
-840,"HeLa, HL60, MV4;11","pEC50 for MV4;11 and HL60 cells: 7.57±0.03 and 6.66±0.05, respectively. pDC50 for Brd4 short/Brd4 long/Brd3/Brd2: 8.1/8.6/7.0/7.4, respectively (24h, HeLa cells). Dmax for Brd4 short/Brd4 long/Brd3/Brd2: 98%/100%/100%/98%, respectively (HeLa cells).",< 2.5 nM,> 98 %
-841,"HeLa, HL60, MV4;11","pEC50 for MV4;11 and HL60 cells: 6.91±0.04 and 5.90±0.05, respectively. pDC50 for Brd4 short/Brd4 long/Brd3/Brd2: 8.4/8.0/6.5/6.7, respectively (24h, HeLa cells). Dmax for Brd4 short/Brd4 long/Brd3/Brd2: 99%/100%/99%/97%, respectively (HeLa cells).",< 4 nM,> 97 %
-842,"HeLa, HL60, MV4;11","pEC50 for MV4;11 and HL60 cells: 7.77±0.06 and 7.46±0.03, respectively. pDC50 for Brd4 short/Brd4 long/Brd3/Brd2: 9.2/9.0/9.1/8.2, respectively (24h, HeLa cells). Dmax for Brd4 short/Brd4 long/Brd3/Brd2: 97%/100%/98%/83%, respectively (HeLa cells).",< 1 nM,> 83 %
-843,"HeLa, HL60, MV4;11","pEC50 for MV4;11 and HL60 cells: 6.24±0.05 and 6.17±0.03, respectively. pDC50 for Brd4 short/Brd4 long/Brd3/Brd2: 6.9/6.7/6.8/NA, respectively (24h, HeLa cells). Dmax for Brd4 short/Brd4 long/Brd3/Brd2: 94%/78%/74%/37%, respectively (HeLa cells).",~ 0.1 uM,
-844,"HeLa, HL60, MV4;11","pEC50 for MV4;11 and HL60 cells: 7.31±0.03 and 6.57±0.02, respectively. pDC50 for Brd4 short/Brd4 long/Brd3/Brd2: 8.1/7.6/7.3/NA, respectively (24h, HeLa cells). Dmax for Brd4 short/Brd4 long/Brd3/Brd2: 98%/95%/91%/43%, respectively (HeLa cells).",~ 7.9 nM,> 90 %
-845,"HeLa, HL60, MV4;11","pEC50 for MV4;11 and HL60 cells: 7.08±0.05 and 6.37±0.03, respectively. pDC50 for Brd4 short/Brd4 long/Brd3/Brd2: 8.1/7.5/7.7/NA, respectively (24h, HeLa cells). Dmax for Brd4 short/Brd4 long/Brd3/Brd2: 95%/93%/92%/26%, respectively (HeLa cells).",~ 7.9 nM,> 90 %
-848,"HeLa, HEK293, U2OS",ITC/SEC/AlphaLISA assays were carried out for CM09/10/11 to confirm the formation of ternary complex in vitro.,< 100 nM,100 %
-853,"MDA-MB-231, A549, A549/DDP, HUVEC","EC50 of PROTAC1: 22.56±1.89uM/25.75±0.91uM/79.51±3.10uM/29.92±1.81uM for MDA-MB-231, A549, A549/DDP, HUVEC cells, respectively (MTT assay, 72h).",,
-854,"MDA-MB-231, A549, A549/DDP, HUVEC","EC50 of PROTAC2: 17.36±1.43uM/31.19±2.95uM/57.55±4.20uM/34.39±2.99uM for MDA-MB-231, A549, A549/DDP, HUVEC cells, respectively (MTT assay, 72h).",,> 80 %
-855,"MDA-MB-231, A549, A549/DDP, HUVEC","EC50 of PROTAC3: 21.32±1.85uM/29.77±0.84uM/30.68±2.45uM/33.92±2.84uM for MDA-MB-231, A549, A549/DDP, HUVEC cells, respectively (MTT assay, 72h).",,
-856,"MDA-MB-231, A549, A549/DDP, HUVEC","EC50 of PROTAC4: 31.67±2.97uM/36.46±0.52uM/>200uM/37.13±2.52uM for MDA-MB-231, A549, A549/DDP, HUVEC cells, respectively (MTT assay, 72h).",,
-859,"HeLa, HEK293",Reported DC50 and Dmax above are in HeLa cells. DC50 for HEK293 cells: 230nM; Dmax for HEK293 cells: 98%. 14a can degrade VHL at higher concentration. See Target UniprotID P40337 for details.,200 nM,88 %
-927,PC9; HCC827; H1975,"EC50: 1.425±0.052uM, 1.874±0.098uM, 1.388±0.556uM for PC9/HCC827/H1975 cells, respectively.",,
-928,PC9; HCC827; H1975,"EC50: 1.117±0.105uM, 1.611±0.139uM, 1.698±0.614uM for PC9/HCC827/H1975 cells, respectively.",,
-929,PC9; HCC827; H1975,"EC50: 0.413±0.087uM, 1.344±0.112uM, 0.657±0.008uM for PC9/HCC827/H1975 cells, respectively.",0.161 uM,68 %
-936,5W1573; NCI-H2030; NCI-H358; HCT116; MIA-PaCa-2,"EC50/DC50/Dmax reported above were obtained using NCI-H2030 cells. DC50: 0.25~0.76uM; Dmax: ~75%-90%, specific value depends on the cell line.",0.59 uM,~ 80 %
-943,SU-DHL-1; H3122,"EC50: 0.058uM/0.18uM/>10uM for SU-DHL-1/H3122/A549 cells, respectively.",,> 90 %
-960,Jurkat; Molt4; Granta-519; Mino; Jeko; Rec1; Maver,"IC50: 25.7nM/7.57nM for CDK4/CDK6, respectively. BSJ-02-162 is capable of degrading both CDK4 and CDK6.",,
-969,Jurkat; Molt4; Granta-519; Mino; Jeko; Rec1; Maver,"IC50: 26.9nM/10.4nM for CDK4/CDK6, respectively. Can degrade both CDK4 and CDK6.",,
-970,Mice primary Sertoli cells and primary Germ cells,"This is an article that use a previously reported PROTAC (PMID: 33062164) as chemical biology tool to investigate the non-enzymatic FAK function in mice. Therefore, the relevant data were not given in this article.",~ 1 nM,~ 100 %
-993,Ba/F3; H1975,EC50: 0.096uM for L858R/T790M mutant EGFR Ba/F3 cells; >10uM for wildtype EGFR Ba/F3 cells,,> 70 %
-997,Ba/F3,Targeting EGFR L858R/T790M mutant,,
-1027,"BxPC3, DLD-1, HCT-116, MDA-MB-231, A549, PC-9","Above EC50 was obtained in BxPC3 cells. EC50 for DLD-1/HCT-116/MDA-MB-231/A549/PC-9 cells: 4.09uM/6.47uM/>10uM/2.42uM/>10uM, respectively.",,
-1028,"BxPC3, DLD-1, HCT-116, MDA-MB-231, A549, PC-9","Above EC50 was obtained in BxPC3 cells. EC50 for DLD-1/HCT-116/MDA-MB-231/A549/PC-9 cells: 5.96uM/2.22uM/>10uM/0.39uM/>10uM, respectively.",,
-1029,"BxPC3, DLD-1, HCT-116, MDA-MB-231, A549, PC-9","Above EC50 was obtained in BxPC3 cells. EC50 for DLD-1/HCT-116/MDA-MB-231/A549/PC-9 cells: 2.04uM/4.39uM/>10uM/0.30uM/>10uM, respectively.",,
-1030,"BxPC3, DLD-1, HCT-116, MDA-MB-231, A549, PC-9","Above EC50 was obtained in BxPC3 cells. EC50 for DLD-1/HCT-116/MDA-MB-231/A549/PC-9 cells: >10uM/>10uM/>10uM/2.14uM/>10uM, respectively.",,
-1073,MOLT4; BT549; HCC1806; COV362; Kuramochi; OVCAR8,IC50 for AZD1175: 1.52±0.17 nM; IC50 for ZNL-02-096: 3.58±0.36 nM,~ 10 nM,
-1155,"BBL358, T47D","Dmax in BBL358/T47D: 8% and 0, respectively.",,8 %
-1156,"BBL358, T47D","Dmax in BBL358/T47D: 40%±27% and 0, respectively.",,40 %
-1163,"BBL358, T47D","Dmax in BBL358/T47D: 3%±3% and 20%±20%, respectively.",,3 %
-1164,"BBL358, T47D","Dmax in BBL358/T47D: 0.5% and 76%, respectively.",,76 %
-1165,"BBL358, T47D","Dmax in BBL358/T47D: 67%±17% and 47%±32%, respectively.",,67 %
-1166,"BBL358, T47D","Dmax in BBL358/T47D: 77%±3% and 82%±10%, respectively.",,77 %
-1167,"BBL358, T47D","Dmax in BBL358/T47D: 93%±5% and 87%±3%, respectively.",,93 %
-1168,"BBL358, T47D","Dmax in BBL358/T47D: 74%±3% and 16%±13%, respectively.",,74 %
-1176,"BBL358, T47D","Dmax in BBL358/T47D: 84%±2% and 89%±2%, respectively.",24 nM,84 %

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models/xgboost_best_model_uniprot_n1.json

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models/xgboost_best_model_uniprot_n2.json

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models/xgboost_cv_model_uniprot_fold0.json

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models/xgboost_cv_model_uniprot_fold1.json

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