Matcha: Multi-Stage Riemannian Flow Matching for Accurate and Physically Valid Molecular Docking

Diffusion models have become a dominant approach to structure-based drug design. However, because they are trained primarily to fit reference structures, they often place ligands in physically implausible poses that clash with the protein. We introduce MLIPDiff, an inference-time guidance method that can be applied to pretrained diffusion models for ligand generation. The method uses physics-informed guidance from UMA (Universal Models for Atoms), a machine-learned interatomic potential (MLIP). The guidance combines four weighted energy terms (protein-ligand interaction, ligand strain, steric clash, and pocket anchoring) and uses the original model checkpoint without retraining. On CrossDocked2020, MLIPDiff completely eliminates protein-ligand collisions while preserving the ligand's local geometry, improving bond-length distributions and physical plausibility relative to the base model. Compared to models such as NucleusDiff that are specifically designed to reduce atomic clashes, MLIPDiff achieves clash-free structures without compromising local geometry. It maintains the base model's PoseBusters pass rate and attains the best median Vina Score, Vina Min, and Vina Dock, surpassing both the base model and NucleusDiff, with a median of 59.6% of ligands per pocket binding more strongly than the reference. MLIPDiff thus addresses a limitation of prior methods by generating physically plausible structures with favorable predicted binding affinity using a single frozen model and no additional training.

All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems. Generating structures at the atomic level of fidelity, however, typically requires expensive iterative diffusion rollouts, making both conventional deployment and inference-time search techniques computationally costly. In this paper, we introduce the Denoiser Cofolding All-Atom Flowmap (DeCAF) framework for distilling state-of-the-art all-atom cofolding models into all-atom flow maps that produce high-quality samples in only a few inference steps. We build DeCAF on a denoiser-based formulation of flow maps with endpoint losses that naturally support SE(3) rigid alignment, which we show is critical for training accurate models. We further derive a simple change of variables that lets DeCAF operate in the σ-space noise schedule of EDM-style architectures, enabling direct distillation from pretrained cofolding diffusion models. Equipped with DeCAF's flowmap lookahead, we introduce a purpose-built inference-time framework that improves sampling through reward-guided search. Empirically, DeCAF-Boltz statistically improves over Boltz-1x in both accuracy (RMSD) and physical validity scores of protein-ligand poses at strict NFE budgets on the challenging Runs N' Poses, while also showing a more optimal Pareto frontier across all inference compute budgets on PoseBusters. Distilling the state-of-the-art Pearl cofolding model, DeCAF-Pearl outperforms diffusion-based cofolding models and matches its teacher on success rate while using 5x fewer NFEs. We release our code at https://github.com/genesistherapeutics/decaf.

Virtual screening performance depends heavily on the chosen docking and scoring methods. Recent AI-based tools such as DiffDock and NMDN have reported strong benchmark results, but their practical utility on realistic, experimentally-derived datasets remains unclear. Here we perform a large-scale evaluation on the LIT-PCBA library (15 targets, 578,295 ligand-target pairs with experimentally confirmed actives and inactives). We compare AutoDock-GPU and DiffDock for pose generation, followed by rescoring with GNINA and NMDN. We further evaluate rank-based consensus strategies and supervised machine learning models trained on docking features. GNINA rescoring of AutoDock-GPU poses (AutoDock-GNINA) emerged as the strongest single method with a median EF1% of 2.14. DiffDock-based approaches underperformed relative to AutoDock-GNINA, particularly on challenging targets such as OPRK1. Carefully designed consensus ranking improved robustness but did not surpass the best single scorer. Supervised ML re-ranking delivered the largest gains, achieving a median EF1% of 4.49 (+110% over AutoDock-GNINA). Our results highlight that even the best classical+ML hybrid workflows provide only modest early enrichment on realistic benchmarks. We conclude that no single docking method dominates across targets and that rigorously validated, cost-effective combinations with supervised re-ranking currently offer the most practical value for virtual screening.