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.

设计具有期望功能的蛋白质可以通过使用 SurfPro 方法来生成具有期望表面和相关生化性质的蛋白质。SurfPro 采用分层编码器逐步建模蛋白质表面的几何形状和生化特征，并使用自回归解码器生成氨基酸序列。我们在标准的逆折叠基准 CATH 4.2 和两个功能蛋白质设计任务（蛋白质结合物设计和酶设计）上评估 SurfPro。我们的 SurfPro 在 CATH 4.2 上实现了 57.78% 的恢复率，并在蛋白质 - 蛋白质结合和酶 - 底物相互作用得分方面取得了更高的成功率。