ProteinGeoBench: Frontier Structural-Biology Agents Are Fluent at Lookup but Lost in Geometry

Matt Turk, Brandon L. Neel, Diana M. Lopez, Zachary D. Smith, Grace N. Johnecheck, James B. Golden · 2026 · arXiv

DOI: 10.48550/arXiv.2610.26829 · open-access PDF

Abstract

Frontier agents retrieve structural metadata well and compute geometry from coordinates less reliably. We ask how much of a benchmark score reflects that gap and how much reflects the evaluation configuration around the model. We study ProteinGeoBench, a suite of 131 protein-structure tasks, using 4,249 rollouts from four frontier models and 4,486 further trials across 26 models. Three of the four frontier models fall within 0.031 of one another (0.785 to 0.816) with no difference between them resolved, while the fourth scores 0.707 and all three gaps to it exclude zero. Three of the four do b

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