DivPro: Diverse protein sequence design with direct structure recovery guidance

Abstract

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