# Protenix-Mini: Efficient Structure Predictor via Compact Architecture, Few-Step Diffusion and Switchable pLM

arXiv: https://arxiv.org/abs/2507.11839 · HTML: https://mlsanity.com/paper/2507.11839/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 14 of its 27 references that are in the map.
- First posted on arXiv 16 Jul 2025.

## Builds on (most cited first, 14 of 14)

- [Denoising Diffusion Implicit Models](https://mlsanity.com/paper/2010.02502/) (2020)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [Flow Straight and Fast: Learning to Generate and Transfer Data with Rectified Flow](https://mlsanity.com/paper/2209.03003/) (2022)
- [Elucidating the Design Space of Diffusion-Based Generative Models](https://mlsanity.com/paper/2206.00364/) (2022)
- [DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Steps](https://mlsanity.com/paper/2206.00927/) (2022)
- [Diffusion Models: A Comprehensive Survey of Methods and Applications](https://mlsanity.com/paper/2209.00796/) (2022)
- [Wide Neural Networks of Any Depth Evolve as Linear Models Under Gradient Descent](https://mlsanity.com/paper/1902.06720/) (2019)
- [InstaFlow: One Step is Enough for High-Quality Diffusion-Based Text-to-Image Generation](https://mlsanity.com/paper/2309.06380/) (2023)
- [Guiding a Diffusion Model with a Bad Version of Itself](https://mlsanity.com/paper/2406.02507/) (2024)
- [Rectified Flow: A Marginal Preserving Approach to Optimal Transport](https://mlsanity.com/paper/2209.14577/) (2022)
- [Inference-Time Scaling for Diffusion Models beyond Scaling Denoising Steps](https://mlsanity.com/paper/2501.09732/) (2025)
- [A Survey on Deep Neural Network Pruning-Taxonomy, Comparison, Analysis, and Recommendations](https://mlsanity.com/paper/2308.06767/) (2023)
- [Are All Layers Created Equal?](https://mlsanity.com/paper/1902.01996/) (2019)
- [Good Subnetworks Provably Exist: Pruning via Greedy Forward Selection](https://mlsanity.com/paper/2003.01794/) (2020)

## Built on by (most cited first, 3 of 3)

- [Proteo-R1: Reasoning Foundation Models for De Novo Protein Design](https://mlsanity.com/paper/2605.02937/) (2026)
- [Protenix-Mini+: efficient structure prediction model with scalable pairformer](https://mlsanity.com/paper/2510.12842/) (2025)
- [ProtDBench: A Unified Benchmark of Protein Binder Design and Evaluation](https://mlsanity.com/paper/2605.04118/) (2026)

## Abstract (arXiv)

Lightweight inference is critical for biomolecular structure prediction and other downstream tasks, enabling efficient real-world deployment and inference-time scaling for large-scale applications. In this work, we address the challenge of balancing model efficiency and prediction accuracy by making several key modifications, 1) Multi-step AF3 sampler is replaced by a few-step ODE sampler, significantly reducing computational overhead for the diffusion module part during inference; 2) In the open-source Protenix framework, a subset of pairformer or diffusion transformer blocks doesn't make contributions to the final structure prediction, presenting opportunities for architectural pruning and lightweight redesign; 3) A model incorporating an ESM module is trained to substitute the conventional MSA module, reducing MSA preprocessing time. Building on these key insights, we present Protenix-Mini, a compact and optimized model designed for efficient protein structure prediction. This streamlined version incorporates a more efficient architectural design with a two-step Ordinary Differential Equation (ODE) sampling strategy. By eliminating redundant Transformer components and refining the sampling process, Protenix-Mini significantly reduces model complexity with slight accuracy drop. Evaluations on benchmark datasets demonstrate that it achieves high-fidelity predictions, with only a negligible 1 to 5 percent decrease in performance on benchmark datasets compared to its full-scale counterpart. This makes Protenix-Mini an ideal choice for applications where computational resources are limited but accurate structure prediction remains crucial.