CC+:在PDB结构和AlphaFold2模型中验证的卷轴线圈的可搜索数据库
Prasun Kumar1, Rokas Petrenas1, William M Dawson1
1School of Chemistry, University of Bristol, Bristol, UK.
Protein science : a publication of the Protein Society
|September 28, 2023
概括
更新后的CC+数据库现在包括超过12,000个经过实验确定的卷轴-卷轴蛋白质结构和120,000个预测的结构,有助于理解蛋白质组装和设计.
科学领域:
- 结构生物学是结构生物学.
- 生物信息学是一种生物信息学.
- 计算生物学是一种计算生物学.
背景情况:
- 阿尔法螺旋螺旋线圈是各种生物过程中涉及的基本蛋白质结构图案.
- 从单独的序列中预测卷轴-卷轴结构可能具有挑战性,而七度重复分析具有局限性.
- 之前开发的SOCKET程序和CC+数据库是为了识别和分析线圈-线圈结构.
研究的目的:
- 更新CC+数据库以新的蛋白质结构和改进的SOCKET分析工具 (Socket2).
- 将 AlphaFold2 预测的结构纳入 CC+ 数据库.
- 为探索卷轴-卷轴组件,它们的序列结构关系和促进蛋白质设计提供全面的资源.
主要方法:
- 使用更新的SOCKET (Socket2) 程序来分析来自蛋白质数据库 (PDB) 的蛋白质结构.
- 在CC+关系数据库中集成实验确定的卷轴结构和AlphaFold2预测的结构.
- 应用了严格的 SOCKET 参数,用于高可靠性线圈-线圈识别.
主要成果:
- 更新的CC+数据库包含大约12,000个经过实验确定的卷轴-卷轴组件.
- 该数据库包括大约12万个潜在的卷轴结构,由AlphaFold2在48个蛋白质组中预测.
- CC+允许在多个层次 (结构,序列,相互作用) 上搜索和可视化卷轴卷轴.
结论:
- 增强的CC+数据库为研究卷轴-卷轴蛋白质结构提供了扩展的资源.
- 集成AlphaFold2预测显著增加了可识别的潜在卷轴线圈的范围.
- CC+ 作为一种有价值的工具,用于理解蛋白质结构-功能关系,并推进蛋白质工程的努力.
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