Closed miquelduranfrigola closed 3 weeks ago
Hi @miquelduranfrigola
I have updated the molecules to the last version and recalculated the Ersilia Features. In the notebook you can find the NP score plots as well as some UMAPs and TSNE. I've only left the best ones. I am now playing with the ADME panel, but will not have anything until Wednesday or Thursday I have not ploted the PCA because we need the updated MOE files.
Fantastic, this is great @GemmaTuron
I have made a temptative on the ADME panel. I think 49 are too many properties, we should reduce to 20 max? The percentile of drugbank approved is the easiest measure to plot for all of them.
The list is: all_props = [ "molecular_weight", "logP", "hydrogen_bond_acceptors", "hydrogen_bond_donors", "Lipinski", "QED", "stereo_centers", "tpsa", "AMES", "BBB_Martins", "Bioavailability_Ma", "CYP1A2_Veith", "CYP2C19_Veith", "CYP2C9_Substrate_CarbonMangels", "CYP2C9_Veith", "CYP2D6_Substrate_CarbonMangels", "CYP2D6_Veith", "CYP3A4_Substrate_CarbonMangels", "CYP3A4_Veith", "Carcinogens_Lagunin", "ClinTox", "DILI", "HIA_Hou", "NR-AR-LBD", "NR-AR", "NR-AhR", "NR-Aromatase", "NR-ER-LBD", "NR-ER", "NR-PPAR-gamma", "PAMPA_NCATS", "Pgp_Broccatelli", "SR-ARE", "SR-ATAD5", "SR-HSE", "SR-MMP", "SR-p53", "Skin_Reaction", "hERG", "Caco2_Wang", "Clearance_Hepatocyte_AZ", "Clearance_Microsome_AZ", "Half_Life_Obach", "HydrationFreeEnergy_FreeSolv", "LD50_Zhu", "Lipophilicity_AstraZeneca", "PPBR_AZ", "Solubility_AqSolDB", "VDss_Lombardo" ]
Sure. I suggest, at least:
you can find all the properties in the figures/adme_props folder - by Monday we should have the list of the 20 selected ones.
These ones I like. Please add yours:
Also, I am surprised about the stereocenters distribution...
Hi @GemmaTuron I would like to try this model for chemical space visualization: eos39co
@GemmaTuron can we close this issue?
yes this is complete. I need to rerun everything with the new datasets though
Hi @GemmaTuron,
In the
data
folder there areall_molecules_$MODEL_ID.csv
files that I calculatedI suggest we do the following plots using a Jupyter Notebook:
⚠️ Please note that Fidele has updated some files and, therefore, I will have to recalculate everything. Files will remain in the same format, so in principle this should not be a big problem.