Cyclic peptide membrane permeability prediction using deep learning model based on molecular attention transformer.

ABSTRACT: Membrane permeability is a critical bottleneck in the development of cyclic peptide drugs. Experimental membrane permeability testing is costly, and precise in silico prediction tools are scarce. In this study, we developed CPMP (https://github.com/panda1103/CPMP), a cyclic peptide membrane permeability prediction model based on the Molecular Attention Transformer (MAT) frame. The model demonstrated robust predictive performance, achieving determination coefficients (R ² ) of 0.67 for PAMPA permeability prediction, and R ² values of 0.75, 0.62, and 0.73 for Caco-2, RRCK, and MDCK cell permeability predictions, respectively. Its performance outperforms traditional machine learning methods and graph-based neural network models. In abla

SUBMITTER: Jiang D 

PROVIDER: S-EPMC11933047 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature