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Yankai Yu

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Open access Jul 2026

PFM: perturbed flow matching for structure-based drug design

A novel method named Perturbed Flow Matching (PFM), which significantly reduces sampling steps by leveraging a Flow Matching framework and introduces a unique perturbed conditional probability path design that incorporates pocket binding site information and atom type-coordinate coupled information to enhance molecular generation performance.

Yankai Yu, Guikun Xu, Zhuyang Xie et al. · 0 citations
Aug 2026

Systematic Benchmarking of AI-Based Molecular Generation Models for Structure-Based Drug Design

A state-aware functional classifier (SAFC) is developed that integrates molecular dynamics derived receptor ensembles, ensemble docking and protein ligand interaction graphs that provides dynamics-aware functional activity rankings for generated molecules that were partly complementary to docking, drug-likeness and synthetic accessibility scores.

H. Kumar, Zhengxiao Yang, Yankai Yu et al. · 0 citations