arXiv:2503.13329cs.LGcs.CE2025-03

PERC工具套件简化冷冻电镜数据整理,助力算法开发。

PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modelling and machine learning

  • 提供三个可独立或组合使用的Python工具包,支持数据下载与处理
  • 实现从PDB/AlphaFold获取结构、懒加载EMPIAR数据、支持冷冻电镜数据增强
  • 适合从事冷冻电镜算法研发的科研人员快速构建数据工作流

数据、工具和模型的易用性推动科学研究。结构生物学领域已有大量公开的实验与模拟数据集。便捷地访问和使用这些数据对高效利用研究资源至关重要。本文介绍一套名为PERC(profet、EMPIARreader和CAKED)的Python软件工具包,用于整合现有公共冷冻电镜数据集或生成新的合成数据集,以支持新型数据处理与解析算法的开发。近年来,基于机器学习的方法在冷冻电镜数据处理与重构中广泛应用。开发此类技术需要大规模数据集,而数据整理常耗时且难以管理。profet可从PDB或AlphaFold数据库便捷下载并裁剪蛋白质序列或结构;EMPIARreader支持以机器学习兼容格式懒加载电子显微镜公共图像档案数据;CAKED则专为电子显微镜数据训练设计,包含特定的数据增强与标注功能。各工具可独立使用,也可作为工作流模块组合。所有工具均开源,且易于扩展以支持更复杂流程。

原文摘要 · Abstract (English)

Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for allowing researchers to make optimal use of their research effort. The tools presented here are useful for collating existing public cryoEM datasets and/or creating new synthetic cryoEM datasets to aid the development of novel data processing and interpretation algorithms. In recent years, structural biology has seen the development of a multitude of machine-learning based algorithms for aiding numerous steps in the processing and reconstruction of experimental datasets and the use of these approaches has become widespread. Developing such techniques in structural biology requires access to large datasets which can be cumbersome to curate and unwieldy to make use of. In this paper we present a suite of Python software packages which we collectively refer to as PERC (profet, EMPIARreader and CAKED). These are designed to reduce the burden which data curation places upon structural biology research. The protein structure fetcher (profet) package allows users to conveniently download and cleave sequences or structures from the Protein Data Bank or Alphafold databases. EMPIARreader allows lazy loading of Electron Microscopy Public Image Archive datasets in a machine-learning compatible structure. The Class Aggregator for Key Electron-microscopy Data (CAKED) package is designed to seamlessly facilitate the training of machine learning models on electron microscopy data, including electron-cryo-microscopy-specific data augmentation and labelling. These packages may be utilised independently or as building blocks in workflows. All are available in open source repositories and designed to be easily extensible to facilitate more advanced workflows if required.

冷冻电镜数据工具机器学习Python工具

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