# CryoAtlas: A Large Curated Dataset and Unified Benchmark for Cryo-EM Atomic Model Building

**Authors:** Mingrui Li, Minzhang Li, Weichen Qin, Yufan Xie, Zhangzhi Xiong, Sixian Shen, Jiakai Zhang, Yuan Pei, Jingyi Yu  
**Lab:** ShanghaiTech University · **Published:** 30 Oct 2026  
**Links:** [arXiv](https://arxiv.org/abs/2610.41411) · [PDF](https://arxiv.org/pdf/2610.41411) · [This page](https://omen-bit.github.io/ai-paper-daily/paper/2610.41411.html)

## Abstract

Deep learning has accelerated automated atomic model building from cryo-EM maps, yet progress remains limited by the lack of large, high-quality datasets and standardized evaluation benchmarks. We address this gap by introducing CryoAtlas, a rigorously curated dataset and unified benchmark for density-guided atomic model building of protein chains. By integrating and filtering EMDB and PDB entries (up to March 2026), CryoAtlas provides 17,809 map-model-sequence entries, including a curated 16,657-entry training split. From this resource, we construct a 618-target benchmark with a shared evaluation protocol that jointly assesses structural accuracy, model-to-map fit, and stereochemical validity. Using this framework, we benchmark state-of-the-art learning-based methods against Phenix and AlphaFold3, comprehensively analyzing the impact of map resolution, sequence length, protein category and sequence identity on modeling accuracy. As a case study, retraining the ModelAngelo CNN component on CryoAtlas improves performance on the benchmark. CryoAtlas provides an open, reproducible foundation for future cryo-EM atomic model building research. Project details and resource release updates are available at https://oulling.github.io/cryoatlas/.

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