KANEL: Kolmogorov-Arnold Network Ensemble Learning Enables Early Hit Enrichment in High-Throughput Virtual Screening

Virtual screening aims to prioritize active compounds from large chemical libraries within a limited experimental budget. When applying Boltz-2 to virtual screening, a key challenge is how to use limited experimental data from the target assay to improve the prioritization of active compounds. We investigated whether fine-tuning the Boltz-2 affinity heads with a small number of binary activity labels could improve early enrichment of active compounds in hit discovery. We compared fine-tuning with 40-300 labels in a retrospective evaluation on eight MF-PCBA targets. With 300 activity measurements, fine-tuning increased the number of actives in the top 1% by a geometric mean of 1.77-fold across the eight targets and improved average precision (AP) by 2.14-fold relative to the control without fine-tuning. We also investigated whether rescoring a subset of candidates could retain the improvement in hit recovery by reranking only the top-ranked Boltz-2 candidates with the fine-tuned head. Restricting rescoring to approximately 10% of the evaluation set retained hit recovery comparable to full rescoring. These findings show that affinity-head fine-tuning with limited activity labels improves early enrichment with Boltz-2 and that this benefit can be retained when rescoring a restricted set of candidates.

Make-on-demand combinatorial synthesis libraries (CSLs) like Enamine REAL have significantly enabled drug discovery efforts. However, their large size presents a challenge for virtual screening, where the goal is to identify the top compounds in a library according to a computational objective (e.g., optimizing docking score) subject to computational constraints under a limited computational budget. For current library sizes -- numbering in the tens of billions of compounds -- and scoring functions of interest, a routine virtual screening campaign may be limited to scoring fewer than 0.1% of the available compounds, leaving potentially many high scoring compounds undiscovered. Furthermore, as constraints (and sometimes objectives) change during the course of a virtual screening campaign, existing virtual screening algorithms typically offer little room for amortization. We propose the approximate-but-exhaustive search protocol for CSLs, or APEX. APEX utilizes a neural network surrogate that exploits the structure of CSLs in the prediction of objectives and constraints to make full enumeration on a consumer GPU possible in under a minute, allowing for exact retrieval of approximate top-k sets. To demonstrate APEX's capabilities, we develop a benchmark CSL comprised of more than 10 million compounds, all of which have been annotated with their docking scores on five medically relevant targets along with physicohemical properties measured with RDKit such that, for any objective and set of constraints, the ground truth top-k compounds can be identified and compared against the retrievals from any virtual screening algorithm. We show APEX's consistently strong performance both in retrieval accuracy and runtime compared to alternative methods.

Accurately ranking active ligands for a target protein pocket from massive chemical libraries remains a central challenge in virtual screening. DrugCLIP and its recent extensions substantially accelerate this process by encoding protein pockets and molecules into a shared embedding space. Despite this progress, further performance improvements typically require retraining the entire model, incurring substantial computational overhead and making target-specific customization inefficient. In this work, we formulate the specialization of pretrained virtual screening models to individual pockets as a test-time adaptation problem and propose PETA, a parameter-efficient framework that directly adapts pretrained model at test time. Given a target pocket, PETA constructs pocket-specific negatives through molecular diffusion and chemical validity filtering, and further moves them toward the reference ligand retrieved from structural databases via embedding-space mixup to create more challenging ranking tasks. A ranking objective then places greater emphasis on suppressing high-scoring invalid candidates that could contaminate the top-ranked screening results, providing structured supervision for lightweight adaptation. Experiments across diverse benchmarks demonstrate that this lightweight, pocket-specific adaptation outperforms both pretrained and fully retrained baselines while updating only the LayerNorm parameters, which account for approximately $0.03\%$ of the full model.