ProtFlow: Flow Matching-based Protein Sequence Design with Comprehensive Protein Semantic Distribution Learning and High-quality Generation

Abstract

Designing protein sequences with desired properties is a fundamental task in protein engineering. Recent advances in deep generative models have greatly accelerated this design process. However, most existing models face the issue of distribution centralization and focus on local compositional statistics of natural sequences instead of the global semantic organization of protein space, which confines their generation to specific regions of the distribution. These problems are amplified for functional proteins, whose sequence patterns strongly correlate with semantic representations and exhibit a long-tailed functional distribution, causing existing models to miss semantic regions associated with rare but essential functions. Here, we propose ProtFlow, a generative model designed for comprehensive semantic distribution learning of protein sequences, enabling high-quality sequence generation. ProtFlow employs a rectified flow matching algorithm to efficiently capture the underlying semantic distribution of the protein design manifold, and introduces a reflow technique enabling one-step sequence generation. We construct a semantic integration network to reorganize the representation space of large protein language models, facilitating stable and compact incorporation of global protein semantics. We pretrain ProtFlow on 2.6M peptide sequences and fine-tune it on antimicrobial peptides (AMPs), a representative class of therapeutic proteins exhibiting unevenly distributed activities across pathogen targets. Experiments show that ProtFlow outperforms state-of-the-art methods in generating high-quality peptides, and AMPs with desirable activity profiles across a range of pathogens, particularly against underrepresented bacterial species. These results demonstrate ProtFlows effectiveness in capturing the full training distribution and its potential as a general framework for computational protein design.