mims-harvard/TDC

PAMPA permeability - new dataset

iwwwish opened this issue · 2 comments

Describe the problem
Currently, TDC has Caco-2 permeability and HIA as the drug absorption tasks. Along with Caco-2, PAMPA (parallel artificial membrane permeability assay) is a commonly employed assay to evaluate drug permeability across the cellular membrane. PAMPA is a non-cell-based and low-cost yet high-throughput alternative to cellular models. Although PAMPA does not model active and efflux transporters, it still provides permeability values that are useful for absorption prediction, because the majority of drugs are absorbed by passive diffusion through the membrane. At NCATS/NIH, compounds are routinely screened in PAMPA and permeability data for 2528 compounds were made public via a PubChem deposition.

References: 1 and 2

Describe the solution you'd like

from tdc.single_pred import ADME
data = ADME(name = PAMPA_Siramshetty')

Additional context
A GCNN model built on a much larger PAMPA dataset (only a subset was made public) is available here.

Thanks Vishal! We would love to work with you on this new ADME task! Let us know how we can help

@kexinhuang12345 I have update the PR description to reflect the latest changes. Happy to provide more details in case needed.