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Updated: Jan 11, 2026

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The ITS2 Database
Published on: March 12, 2012
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PASS2:更新基于结构的序列对齐数据库
Revathy Menon1, Soumya Nayak1, Rama Rajesh2
1National Centre for Biological Sciences (Tata Institute of Fundamental Research), GKVK Campus, Bellary Road, Bangalore, Karnataka 560065, India.
Database : the journal of biological databases and curation
|November 13, 2025
概括
作为结构超级家族组织的蛋白质对齐 (PASS2) 数据库现在包括26,690个蛋白质域的基于结构的序列对齐. 此更新增强了使用最新的蛋白质结构分类扩展 (SCOPe) 框架的进化建模和蛋白质家族识别.
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:
- 蛋白质序列对齐对于理解蛋白质进化和功能至关重要.
- 由于其低序列相同性,对与远距离相关的蛋白质进行对齐是具有挑战性的.
- 结构信息可以指导分离的蛋白质序列的准确对齐.
研究的目的:
- 更新和增强作为结构超级家族组织的蛋白质对齐 (PASS2) 数据库.
- 为超级家族内的蛋白质域提供基于结构的序列对齐.
- 整合新的功能,以改善蛋白质关系和相互作用的分析.
主要方法:
- 使用蛋白质结构分类扩展 (SCOPe) 框架 (版本2.08).
- 对蛋白质域进行结构引导的序列对齐,其序列相同性<40%.
- 采用k-means集群来划分分歧的超级家族和确定保存的相互作用.
主要成果:
- PASS2.8数据库包含了26690个蛋白质域在2058个超级家族中的对齐.
- 包括保存的二次结构图案,隐藏的马尔科夫模型 (HMM) 和保存的残留物.
- 添加了拓图,潜在交互体,并更新了保守交互方法.
结论:
- 更新的PASS2数据库为分析蛋白质超级家族提供了有价值的基于结构的对齐和特征.
- 促进进化研究,蛋白质功能预测和实验设计.
- 这些新功能提供了对蛋白质域关系和相互作用的更深入的见解.
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