DCFold: Efficient Protein Structure Generation with Single Forward Pass

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.

Protein function relies on dynamic conformational ensembles, yet current generative models like AlphaFold3 often fail to produce ensembles that match experimental data. Recent experiment-guided generators attempt to address this by steering the reverse diffusion process. However, these methods are limited by fixed sampling horizons and sensitivity to initialization, often yielding thermodynamically implausible results. We introduce a general inference-time optimization framework to solve these challenges. First, we optimize over latent representations to maximize ensemble log-likelihood, rather than perturbing structures post hoc. This approach eliminates dependence on diffusion length, removes initialization bias, and easily incorporates external constraints. Second, we present novel sampling schemes for drawing Boltzmann-weighted ensembles. By combining structural priors from AlphaFold3 with force-field-based priors, we sample from their product distribution while balancing experimental likelihoods. Our results show that this framework consistently outperforms state-of-the-art guidance, improving diversity, physical energy, and agreement with data in X-ray crystallography and NMR, often fitting the experimental data better than deposited PDB structures. Finally, inference-time optimization experiments maximizing ipTM scores reveal that perturbing AlphaFold3 embeddings can artificially inflate model confidence. This exposes a vulnerability in current design metrics, whose mitigation could offer a pathway to reduce false discovery rates in binder engineering.

Diffusion- and flow-based generative models have recently demonstrated strong performance in protein backbone generation tasks, offering unprecedented capabilities for de novo protein design. However, despite their generation quality, these models are constrained by slow sampling, often requiring hundreds of iterative steps. This computational bottleneck limits their practical utility in large-scale protein discovery, where thousands to millions of candidate structures are needed. To address this challenge, we explore the techniques of score distillation, which has shown great success in reducing the number of sampling steps in the vision domain while maintaining high generation quality. However, a straightforward adaptation of these methods results in unacceptably low designability. We introduce Score Protein identity Distillation (SPID), which resolves this incompatibility by combining few-step generation with inference-time noise scaling. SPID adapts the Score identity Distillation (SiD) framework to both diffusion- and flow-based models without requiring access to pretraining data. Applied to the Proteina flow-matching model, our 16-step generator achieves 94.4% designability, matching the 400-step teacher, while delivering more than a 20-fold reduction in effective backbone-generation time and maintaining comparable diversity and novelty. SPID generalizes across unconditional generation, fold-class conditional generation, and motif scaffolding, and extends to equivariant diffusion architectures, achieving significant reduction in generation time with comparable generation quality to the teacher in all tasks. The resulting reduction in inference cost could facilitate large-scale in silico protein design, thereby advancing diffusion-based models toward real-world protein engineering applications. The PyTorch implementation is available at https://github.com/LY-Xie/SiD_Protein