Additional file 1 of One class classification for the detection of β2 adrenergic receptor agonists using single-ligand dynamic interaction data
Creators: name: Chiesa, Luca
name: Kellenberger, Esther
Publisher: name: figshare
Year: 2022
Subjects: subject: Biophysics
subject: Biochemistry
subject: Molecular Biology
subject: Pharmacology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences

description: Additional file 1: Figure S1. Average and crystallographic interaction fingerprints for the three reference agonists. Figure S2. RMSD of the binding site residues during the simulation of the BI167107-ADRB2 complex. Figure S3. Pairwise RMSD of the four reference trajectories. Figure S4. Pairwise RMSD of the representative structures used for docking. Figure S5. RMSD of the binding site residues during the simulation of the epinephrine-ADRB2 complex. Figure S6. RMSD of the binding site residues during the simulation of the HBI-ADRB2 complex. Table S1. Annotated list of molecules from the agonist/antagonist dataset. Table S2. Annotated list of molecules from the agonist/inactive dataset. Table S3. Average performances of the OCSVM models on the agonist/antagonist dataset, from docking data obtained using the representative structures. Table S4. Performances of the OCSVM models on the agonist/antagonist dataset, from docking data obtained using crystallographic structures. Table S5. Average performances of the OCSVM models on the agonist/inactive dataset, from docking data obtained using the representative structures. Table S6. Performances of the OCSVM models on the agonist/inactive dataset, from docking data obtained using crystallographic structures. Table S7. Average performances of shorter trajectories of epinephrine-based OCSVM models on the agonist-antagonist dataset, from docking data obtained using the representative structures. Table S8. Performances of shorter trajectories of epinephrine-based OCSVM models on the agonist-antagonist dataset, from docking data obtained using crystallographic structures. Table S9. Average performances of shorter trajectories of HBI-based OCSVM models on the agonist-antagonist dataset, from docking data obtained using the representative structures. Table S10. Performances of shorter trajectories of HBI-based OCSVM models on the agonist-antagonist dataset, from docking data obtained using crystallographic structures. Table S11. Average performances of the combined dataset OCSVM models on the agonist-antagonist dataset, from docking data obtained using the representative structures. Table S12. Performances of the combined dataset OCSVM models on the agonist-antagonist dataset, from docking data obtained using crystallographic structures. Table S13. Average performance of GRIM at different thresholds on the agonist-antagonist dataset, from docking data obtained using the representative structures. Default definition of hydrophobic contacts. Table S14. Performance of GRIM at different thresholds on the agonist-antagonist dataset, from docking data obtained using crystallographic structures. Default definition of hydrophobic contacts. Table S15. Average performance of GRIM at different thresholds on the agonist-antagonist dataset, from docking data obtained using the representative structures. Newhyd definition of hydrophobic contacts. Table S16. Performance of GRIM at different thresholds on the agonist-antagonist dataset, from docking data obtained using crystallographic structures. Newhyd definition of hydrophobic contacts. Table S17. Average performance of GRIM at different thresholds on the agonist-inactive dataset, from docking data obtained using the representative structures. Default definition of hydrophobic contacts. Table S18. Performance of GRIM at different thresholds on the agonist-inactive dataset, from docking data obtained using crystallographic structures. Default definition of hydrophobic contacts. Table S19. Average performance of GRIM at different thresholds on the agonist-inactive dataset, from docking data obtained using the representative structures. Newhyd definition of hydrophobic contacts. Table S20. Performance of GRIM at different thresholds on the agonist-inactive dataset, from docking data obtained using crystallographic structures. Newhyd definition of hydrophobic contacts. Table S21. Average optimal threshold for agonist/antagonist classification for GRIM, IFP, and 3D pharmacophore. Table S22. Interaction graphs statistics from the four reference trajectories. Table S23. Interaction graphs statistics form the docking poses of the agonist-antagonist dataset and agonist-inactive datasets.