Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design

TL;DR

This paper introduces a new high-quality synthetic protein dataset and a unified framework that significantly enhances the diversity and co-designability of de novo protein design models by aligning synthetic sequences with structures.

Contribution

The authors created a novel synthetic dataset aligned with experimental favorability and structural recoverability, improving state-of-the-art protein design models' diversity and co-designability.

Findings

+54% in structural diversity for La-Proteina

+27% in co-designability for La-Proteina

+73% in structural diversity for Proteina Atomistica

Abstract

High-quality training datasets are crucial for the development of effective protein design models, but existing synthetic datasets often include unfavorable sequence-structure pairs, impairing generative model performance. We leverage ProteinMPNN, whose sequences are experimentally favorable as well as amenable to folding, together with structure prediction models to align high-quality synthetic structures with recoverable synthetic sequences. In that way, we create a new dataset designed specifically for training expressive, fully atomistic protein generators. By retraining La-Proteina, which models discrete residue type and side chain structure in a continuous latent space, on this dataset, we achieve new state-of-the-art results, with improvements of +54% in structural diversity and +27% in co-designability. To validate the broad utility of our approach, we further introduce Proteina Atomistica, a unified flow-based framework that jointly learns the distribution of protein backbone structure, discrete sequences, and atomistic side chains without latent variables. We again find that training on our new sequence-structure data dramatically boosts benchmark performance, improving \method's structural diversity by +73% and co-designability by +5%. Our work highlights the critical importance of aligned sequence-structure data for training high-performance de novo protein design models. Our new dataset https://catalog.ngc.nvidia.com/orgs/nvidia/teams/clara/resources/proteina-atomistica_data/files?version=release , the Consistency Distilled Synthetic Protein Database, is made available as an open-source resource.