DivPro: diverse protein sequence design with direct structure recovery guidance

TL;DR

DivPro is a new method for designing diverse protein sequences that fold into the same structure, using structure prediction to guide the design process.

Contribution

DivPro introduces a probabilistic sequence space model that improves diversity while maintaining structural accuracy.

Findings

DivPro generates diverse sequences that fold into target structures with high accuracy.

The model outperforms existing methods in sequence diversity while maintaining structural fidelity.

Structure prediction models like AlphaFold2 confirm the reliability of designed sequences.

Abstract

Structure-based protein design is crucial for designing proteins with novel structures and functions, which aims to generate sequences that fold into desired structures. Current deep learning-based methods primarily focus on training and evaluating models using sequence recovery-based metrics. However, this approach overlooks the inherent ambiguity in the relationship between protein sequences and structures. Relying solely on sequence recovery as a training objective limits the models’ ability to produce diverse sequences that maintain similar structures. These limitations become more pronounced when dealing with remote homologous proteins, which share functional and structural similarities despite low-sequence identity.

Here, we present DivPro, a model that learns to design diverse sequences that can fold into similar structures. To improve sequence diversity, instead of learning a single fixed sequence representation for an input structure as in existing methods, DivPro learns a probabilistic sequence space from which diverse sequences could be sampled. We leverage the recent advancements in in silico protein structure prediction. By incorporating structure prediction results as training guidance, DivPro ensures that sequences sampled from this learned space reliably fold into the target structure. We conducted extensive experiments on three sequence design benchmarks and evaluated the structures of designed sequences using structure prediction models including AlphaFold2. Results show that DivPro can maintain high structure recovery while significantly improving the sequence diversity.

The source code and datasets are available at https://github.com/veghen/DivPro.

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