# Protenix-Mini+: efficient structure prediction model with scalable pairformer

arXiv: https://arxiv.org/abs/2510.12842 · HTML: https://mlsanity.com/paper/2510.12842/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 20 of its 38 references that are in the map.
- First posted on arXiv 13 Oct 2025.

## Builds on (most cited first, 20 of 20)

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- [DPM-Solver: A Fast ODE Solver for Diffusion Probabilistic Model Sampling in Around 10 Steps](https://mlsanity.com/paper/2206.00927/) (2022)
- [Consistency Models](https://mlsanity.com/paper/2303.01469/) (2023)
- [Transformers are SSMs: Generalized Models and Efficient Algorithms Through Structured State Space Duality](https://mlsanity.com/paper/2405.21060/) (2024)
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- [A Survey on Deep Neural Network Pruning-Taxonomy, Comparison, Analysis, and Recommendations](https://mlsanity.com/paper/2308.06767/) (2023)
- [SE(3)-Stochastic Flow Matching for Protein Backbone Generation](https://mlsanity.com/paper/2310.02391/) (2023)
- [The Hedgehog & the Porcupine: Expressive Linear Attentions with Softmax Mimicry](https://mlsanity.com/paper/2402.04347/) (2024)
- [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)
- [Pad'e Activation Units: End-to-end Learning of Flexible Activation Functions in Deep Networks](https://mlsanity.com/paper/1907.06732/) (2019)
- [Protenix-Mini: Efficient Structure Predictor via Compact Architecture, Few-Step Diffusion and Switchable pLM](https://mlsanity.com/paper/2507.11839/) (2025)

## Abstract (arXiv)

Lightweight inference is critical for biomolecular structure prediction and downstream tasks, enabling efficient real-world deployment and inference-time scaling for large-scale applications. While AF3 and its variants (e.g., Protenix, Chai-1) have advanced structure prediction results, they suffer from critical limitations: high inference latency and cubic time complexity with respect to token count, both of which restrict scalability for large biomolecular complexes. To address the core challenge of balancing model efficiency and prediction accuracy, we introduce three key innovations: (1) compressing non-scalable operations to mitigate cubic time complexity, (2) removing redundant blocks across modules to reduce unnecessary overhead, and (3) adopting a few-step sampler for the atom diffusion module to accelerate inference. Building on these design principles, we develop Protenix-Mini+, a highly lightweight and scalable variant of the Protenix model. Within an acceptable range of performance degradation, it substantially improves computational efficiency. For example, in the case of low-homology single-chain proteins, Protenix-Mini+ experiences an intra-protein LDDT drop of approximately 3% relative to the full Protenix model -- an acceptable performance trade-off given its substantially 90%+ improved computational efficiency.