A curated multi-endpoint drug-protein bioactivity dataset with construct-aware protein targets

Understanding how drugs interact with protein targets is fundamental to drug discovery, drug repurposing and the early identification of promising therapeutic candidates before costly experimental testing. Sequence-based DTI models face three practical limitations: labelled interactions are scarce and unevenly distributed, large pretrained chemical and protein encoders are expensive to fine-tune end-to-end, and independently encoded sequences do not capture pair-specific dependencies. We present BERT4DTI, which encodes SMILES strings with ChemBERTa and amino-acid sequences with ProtBERT, applies bidirectional mutual attention between token-level representations, and classifies the resulting interaction features using convolutional layers and a multilayer perceptron. To reduce trainable size, ProtBERT is truncated to 18 retained layers and only the last two layers of each encoder are fine-tuned. On BIOSNAP, DAVIS and BindingDB, BERT4DTI is competitive, achieving the best ROC-AUC and PR-AUC on BIOSNAP and the highest sensitivity on all three benchmarks. An ablation on DAVIS shows that mutual attention improves PR-AUC and specificity. With 125M trainable parameters compared with 353M for full BERT fine-tuning, BERT4DTI provides a favourable performance-parameter trade-off for sequence-based DTI screening, while leaving runtime profiling, calibration and leakage-audited validation for future work.

Predictive models in biomedicine depend on structured assay data locked in the text, tables, and supplements of primary publications. This bottleneck is especially acute in targeted protein degradation (TPD), where each assay record must combine compound identity, degradation target, recruiter, assay context, and endpoint values reported across sections, tables, and supplementary files. Inconsistent compound identifiers and incomplete or implicit assay context further demand domain-specific logic that generic LLM pipelines do not provide. Existing molecular glue and PROTAC databases are manually curated and often lack the experimental context required for downstream modeling. We formulate TPD database extraction as a domain-specific curation task and present an expert-in-the-loop LLM workflow, evaluated through a triangular comparison among LLM predictions, standardized baseline records, and expert-annotated ground truth. A lightweight cross-validated prompt-refinement module adapts extraction instructions from scarce expert annotations. With only seven annotated molecular glue publications, the workflow achieved record-level $F_1 = 0.98$ and transferred to PROTACs by terminology substitution alone, maintaining record-level $F_1 > 0.93$. Applied at scale, it expanded molecular glue and PROTAC databases by 81% and 92% records, respectively, with 92% and 82.5% of newly recovered records validated as correct upon expert review. The workflow also recovered kinetic and assay-context information essential for cross-study potency comparison and condition-aware degradation modeling. We release the workflow, prompts, evaluation code, and extracted datasets as resources for TPD data curation and AI-assisted scientific curation more broadly.

Protein-ligand bioactivity data published in the literature are essential for drug discovery, yet manual curation struggles to keep pace with rapidly growing literature. Automated bioactivity extraction remains challenging because it requires not only interpreting biochemical semantics distributed across text, tables, and figures, but also reconstructing chemically exact ligand structures (e.g., Markush structures). To address this bottleneck, we introduce BioMiner, a multi-modal extraction framework that explicitly separates bioactivity semantic interpretation from ligand structure construction. Within BioMiner, bioactivity semantics are inferred through direct reasoning, while chemical structures are resolved via a chemical-structure-grounded visual semantic reasoning paradigm, in which multi-modal large language models operate on chemically grounded visual representations to infer inter-structure relationships, and exact molecular construction is delegated to domain chemistry tools. For rigorous evaluation and method development, we further establish BioVista, a comprehensive benchmark comprising 16,457 bioactivity entries curated from 500 publications. BioMiner validates its extraction ability and provides a quantitative baseline, achieving an F1 score of 0.32 for bioactivity triplets. BioMiner's practical utility is demonstrated via three applications: (1) extracting 82,262 data from 11,683 papers to build a pre-training database that improves downstream models performance by 3.9%; (2) enabling a human-in-the-loop workflow that doubles the number of high-quality NLRP3 bioactivity data, helping 38.6% improvement over 28 QSAR models and identification of 16 hit candidates with novel scaffolds; and (3) accelerating protein-ligand complex bioactivity annotation, achieving a 5.59-fold speed increase and 5.75% accuracy improvement over manual workflows in PoseBusters dataset.