# Floating Anchor Diffusion Model for Multi-motif Scaffolding

arXiv: https://arxiv.org/abs/2406.03141 · HTML: https://mlsanity.com/paper/2406.03141/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 33 references that are in the map.
- First posted on arXiv 5 Jun 2024.

## Builds on (most cited first, 7 of 7)

- [Maximum Likelihood Training of Score-Based Diffusion Models](https://mlsanity.com/paper/2101.09258/) (2021)
- [Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem](https://mlsanity.com/paper/2206.04119/) (2022)
- [Riemannian Score-Based Generative Modelling](https://mlsanity.com/paper/2202.02763/) (2022)
- [SE(3) diffusion model with application to protein backbone generation](https://mlsanity.com/paper/2302.02277/) (2023)
- [Protein Design with Guided Discrete Diffusion](https://mlsanity.com/paper/2305.20009/) (2023)
- [Riemannian Diffusion Models](https://mlsanity.com/paper/2208.07949/) (2022)
- [De novo protein design using geometric vector field networks](https://mlsanity.com/paper/2310.11802/) (2023)

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

- [DiffGraph: An Automated Agent-driven Model Merging Framework for In-the-Wild Text-to-Image Generation](https://mlsanity.com/paper/2603.20470/) (2026)
- [Flash Invariant Point Attention](https://mlsanity.com/paper/2505.11580/) (2025)
- [EnzyControl: Adding Functional and Substrate-Specific Control for Enzyme Backbone Generation](https://mlsanity.com/paper/2510.25132/) (2025)

## Abstract (arXiv)

Motif scaffolding seeks to design scaffold structures for constructing proteins with functions derived from the desired motif, which is crucial for the design of vaccines and enzymes. Previous works approach the problem by inpainting or conditional generation. Both of them can only scaffold motifs with fixed positions, and the conditional generation cannot guarantee the presence of motifs. However, prior knowledge of the relative motif positions in a protein is not readily available, and constructing a protein with multiple functions in one protein is more general and significant because of the synergies between functions. We propose a Floating Anchor Diffusion (FADiff) model. FADiff allows motifs to float rigidly and independently in the process of diffusion, which guarantees the presence of motifs and automates the motif position design. Our experiments demonstrate the efficacy of FADiff with high success rates and designable novel scaffolds. To the best of our knowledge, FADiff is the first work to tackle the challenge of scaffolding multiple motifs without relying on the expertise of relative motif positions in the protein. Code is available at https://github.com/aim-uofa/FADiff.