SurfPro: Functional Protein Design Based on Continuous Surface
<|reference_start|>SurfPro: Functional Protein Design Based on Continuous Surface: How can we design proteins with desired functions? We are motivated by a chemical intuition that both geometric structure and biochemical properties are critical to a protein's function. In this paper, we propose SurfPro, a new method to generate functional proteins given a desired surface and its associated biochemical properties. SurfPro comprises a hierarchical encoder that progressively models the geometric shape and biochemical features of a protein surface, and an autoregressive decoder to produce an amino acid sequence. We evaluate SurfPro on a standard inverse folding benchmark CATH 4.2 and two functional protein design tasks: protein binder design and enzyme design. Our SurfPro consistently surpasses previous state-of-the-art inverse folding methods, achieving a recovery rate of 57.78% on CATH 4.2 and higher success rates in terms of protein-protein binding and enzyme-substrate interaction scores.<|reference_end|>
@article{song2024surfpro:,
    title={SurfPro: Functional Protein Design Based on Continuous Surface},
    author={Zhenqiao Song, Tinglin Huang, Lei Li, Wengong Jin},
    journal={arXiv preprint arXiv:2405.06693},
    year={2024},
    archivePrefix={arXiv},
    eprint={2405.06693},
    primaryClass={q-bio.BM cs.LG}
}