蛋白质家族,域和站点的PROSITE数据库
Christian J A Sigrist1, Béatrice A Cuche1, Edouard de Castro1
1Swiss-Prot Group, Swiss Institute of Bioinformatics (SIB), Centre Médical Universitaire (CMU), 1 rue Michel Servet, CH-1211 Geneva 4, Switzerland.
Nucleic acids research
|November 20, 2025
概括
蛋白质域数据库PROSITE现在集成AlphaFold结构并优化其搜索工具. 更新增强了SARS-CoV-2的研究,并揭示了新的转录因子链接.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 分子生物学分子生物学
背景情况:
- PROSITE是蛋白质域,家族和功能站点的关键数据库,使用模式和配置文件进行识别.
- ProRule通过关键的氨基酸信息增强了PROSITE的配置文件,有助于对UniProtKB/Swiss-Prot条目进行注释.
- PROSITE在SARS-CoV-2研究中发挥了重要作用,开发了病毒蛋白域的新工具和配置文件.
研究的目的:
- 更新和增强PROSITE数据库及其相关工具,以改善蛋白质注释和研究.
- 纳入新的数据源,如AlphaFold结构和本体,以更准确地定义域边界和特征注释.
- 提高PROSITE搜索功能的性能和可用性,特别是用于大规模的生物数据分析.
主要方法:
- 利用现有的PROSITE工具,为SARS-CoV-2蛋白域开发新的配置文件/ProRules.
- 将ChEBI本体学和Rhea参考词汇整合到ProRule中,用于化学联体和生物化学反应注释.
- 使用AlphaFold预测的3D结构来定义域边界并增强ScanProsite可视化.
- 重写和优化多核处理器的pfsearch代码,使用新的启发式来提高性能.
主要成果:
- PROSITE为SARS-CoV-2研究做出了贡献,并确定了POU2F和NF-κB转录因子协调器之间的联系.
- 现在ProRule包括了ChEBI和Rhea词汇,改善了对联体和反应的注释.
- AlphaFold结构用于域边界定义,ScanProsite允许对这些结构进行可视化.
- 对于现代硬件的速度和效率,pfsearch代码得到了显著的优化.
结论:
- PROSITE继续发展,为蛋白质域分析提供了必不可少的资源,并支持像病毒学这样的关键研究领域.
- 集成AlphaFold结构和增强的搜索功能提高了PROSITE注释的准确性和实用性.
- 持续的发展确保PROSITE仍然是生物信息学社区的一种强大而有效的工具.
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