DEL-Ranking: Ranking-Correction Denoising Framework for Elucidating Molecular Affinities in DNA-Encoded Libraries

DNA-encoded library (DEL) screening has revolutionized protein-ligand binding detection, enabling rapid exploration of vast chemical spaces through read count analysis. However, two critical challenges limit its effectiveness: distribution noise in low copy number regimes and systematic shifts between read counts and true binding affinities. We present DEL-Ranking, a comprehensive framework that simultaneously addresses both challenges through innovative rankingbased denoising and activity-referenced correction. Our approach introduces a dual-perspective ranking strategy combining Pair-wise Soft Rank (PSR) and Listwise Global Rank (LGR) constraints to preserve both local and global count relationships. Additionally, we develop an Activity-Referenced Correction (ARC) module that bridges the gap between read counts and binding affinities through iterative refinement and biological consistency enforcement. Another key contribution of this work is the curation and release of three comprehensive DEL datasets that uniquely combine ligand 2D sequences, 3D conformational information, and experimentally validated activity labels. We validate our framework on five diverse DEL datasets and introduce three new comprehensive datasets featuring 2D sequences, 3D structures, and activity labels. DEL-Ranking achieves state-of-the-art performance across multiple correlation metrics and demonstrates strong generalization ability across different protein targets. Importantly, our approach successfully identifies key functional groups associated with binding affinity, providing actionable insights for drug discovery.