FLOWR.ROOT – A flow matching-based foundation model for joint multi-purpose structure-aware 3D ligand generation and affinity prediction

Abstract We present FLOWR.ROOT, an S E (3)-equivariant flow-matching foundation model that unifies pocket-aware 3D ligand generation with multi-endpoint binding affinity prediction (pIC 50 , p K i , p K d , pEC 50 ) and pLDDT-based confidence estimation in a single backbone. One trained model supports de novo pocket-conditional generation, interaction- and pharmacophore-conditional sampling, scaffold hopping and elaboration, and fragment growing or replacement, enabled by a mixed isotropic–anisotropic prior placement strategy. Training proceeds in three stages: large-scale pre-training on billions of ligand conformations and millions of mixed-fidelity protein–ligand complexes, refinement on curated co-crystal data, and project-specific adaptation via parameter-efficient LoRA finetuning. Joint structure–affinity modelling enables inference-time importance-sampling guidance for single- and multi-objective design without external scoring functions. Case studies on kinase selectivity (CK2 α /CLK3) and scaffold elaboration on TYK2, ER α , and BACE1 illustrate utility from hit identification through lead optimization.