# HelixFold-Multimer: Elevating Protein Complex Structure Prediction to New Heights

arXiv: https://arxiv.org/abs/2404.10260 · HTML: https://mlsanity.com/paper/2404.10260/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 3 of its 25 references that are in the map.
- First posted on arXiv 16 Apr 2024.

## Builds on (most cited first, 3 of 3)

- [Independent SE(3)-Equivariant Models for End-to-End Rigid Protein Docking](https://mlsanity.com/paper/2111.07786/) (2021)
- [HelixFold-Single: MSA-free Protein Structure Prediction by Using Protein Language Model as an Alternative](https://mlsanity.com/paper/2207.13921/) (2022)
- [HelixFold: An Efficient Implementation of AlphaFold2 using PaddlePaddle](https://mlsanity.com/paper/2207.05477/) (2022)

## Built on by (most cited first, 2 of 2)

- [Technical Report of HelixFold3 for Biomolecular Structure Prediction](https://mlsanity.com/paper/2408.16975/) (2024)
- [HelixDesign-Antibody: A Scalable Production-Grade Platform for Antibody Design Built on HelixFold3](https://mlsanity.com/paper/2507.02345/) (2025)

## Abstract (arXiv)

While monomer protein structure prediction tools boast impressive accuracy, the prediction of protein complex structures remains a daunting challenge in the field. This challenge is particularly pronounced in scenarios involving complexes with protein chains from different species, such as antigen-antibody interactions, where accuracy often falls short. Limited by the accuracy of complex prediction, tasks based on precise protein-protein interaction analysis also face obstacles. In this report, we highlight the ongoing advancements of our protein complex structure prediction model, HelixFold-Multimer, underscoring its enhanced performance. HelixFold-Multimer provides precise predictions for diverse protein complex structures, especially in therapeutic protein interactions. Notably, HelixFold-Multimer achieves remarkable success in antigen-antibody and peptide-protein structure prediction, greatly surpassing AlphaFold 3. HelixFold-Multimer is now available for public use on the PaddleHelix platform, offering both a general version and an antigen-antibody version. Researchers can conveniently access and utilize this service for their development needs.