Diffusion Model with Representation Alignment for Protein Inverse Folding

TL;DR

This paper introduces DMRA, a novel diffusion model with representation alignment for protein inverse folding, improving sequence prediction accuracy by capturing inter-residue relationships and aligning semantic representations.

Contribution

The paper proposes a new diffusion-based approach with representation alignment that enhances protein inverse folding by aggregating contextual information and normalizing residue representations.

Findings

Achieves state-of-the-art performance on CATH4.2 dataset

Demonstrates strong generalization on TS50 and TS500 datasets

Outperforms existing methods in accuracy and robustness

Abstract

Protein inverse folding is a fundamental problem in bioinformatics, aiming to recover the amino acid sequences from a given protein backbone structure. Despite the success of existing methods, they struggle to fully capture the intricate inter-residue relationships critical for accurate sequence prediction. We propose a novel method that leverages diffusion models with representation alignment (DMRA), which enhances diffusion-based inverse folding by (1) proposing a shared center that aggregates contextual information from the entire protein structure and selectively distributes it to each residue; and (2) aligning noisy hidden representations with clean semantic representations during the denoising process. This is achieved by predefined semantic representations for amino acid types and a representation alignment method that utilizes type embeddings as semantic feedback to normalize each residue. In experiments, we conduct extensive evaluations on the CATH4.2 dataset to demonstrate that DMRA outperforms leading methods, achieving state-of-the-art performance and exhibiting strong generalization capabilities on the TS50 and TS500 datasets.