建立标准化蛋白设计评测基准，解决方法可比性难题
MotifBench: A standardized protein design benchmark for motif-scaffolding problems
- 定义统一评估流程与指标，确保结果可比较
- 包含30个高难度测试题，部分已有解但现有方法失败
- 开源代码与排行榜，推动蛋白设计领域进步
motif-scaffolding 是计算蛋白设计的核心任务：给定一个具有特定几何结构以实现所需生化功能的原子坐标（称为 motif），目标是寻找包含该 motif 且保持其几何形状的多样化蛋白结构（scaffold）。近年来，得益于可靠的蛋白结构预测和固定骨架序列设计方法，该领域取得显著进展。然而，不同研究采用的评估策略差异大，导致结果难以比较、复现困难，阻碍了稳健发展。为此，我们提出 MotifBench，包含三部分：(1) 精确指定的流程与评估指标，(2) 30 个基准测试问题，(3) 在 github.com/blt2114/MotifBench 的实现与排行榜。这些测试用例比早期基准更具挑战性，其中一些问题已有已知解，但据我们所知，当前最先进方法未能找到任何解。
原文摘要 · Abstract (English)
The motif-scaffolding problem is a central task in computational protein design: Given the coordinates of atoms in a geometry chosen to confer a desired biochemical function (a motif), the task is to identify diverse protein structures (scaffolds) that include the motif and maintain its geometry. Significant recent progress on motif-scaffolding has been made due to computational evaluation with reliable protein structure prediction and fixed-backbone sequence design methods. However, significant variability in evaluation strategies across publications has hindered comparability of results, challenged reproducibility, and impeded robust progress. In response we introduce MotifBench, comprising (1) a precisely specified pipeline and evaluation metrics, (2) a collection of 30 benchmark problems, and (3) an implementation of this benchmark and leaderboard at github.com/blt2114/MotifBench. The MotifBench test cases are more difficult compared to earlier benchmarks, and include protein design problems for which solutions are known but on which, to the best of our knowledge, state-of-the-art methods fail to identify any solution.
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