Effect of broader literature retrieval on permeability-modeling conclusions

Determine whether broader retrieval of published PROTAC PAMPA measurements would change the conclusions about permeability modeling, given that reported PAMPA data is dominated by optimization series around fixed scaffolds and therefore may have a small effective sample size.

Background

The study expands the publicly available PROTAC PAMPA dataset but acknowledges that its literature search covered only 124 articles and was intended as a proof of concept. Although broader retrieval could increase the number of records, the authors question whether it would alter the modeling conclusions because published measurements are concentrated in closely related optimization series around fixed scaffolds. The unresolved issue is therefore whether additional literature coverage would provide genuinely independent chemical information and improve the generalizability of permeability models, rather than merely adding correlated analogues.

References

However, we are not sure broader retrieval would change the modeling conclusion: reported PAMPA is dominated by optimization series around fixed scaffolds, thus affecting the effective sample size.

— The Challenges of PROTAC Permeability Prediction  (2610.07998 - Hudec et al., 6 Oct 2026) in Section 4, “Limitations and future work”