CPIExtract:一个软件包,用于收集和协调小分子和蛋白质相互作用
Andrea Piras1, Shi Chenghao2, Michael Sebek2
1Department of Electronics, Information and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci, 32, 20133, Milan, Italy.
bioRxiv : the preprint server for biology
|July 15, 2024
概括
CPIExtract从多个数据库中协调分散的化合物-蛋白质相互作用数据. 该工具显著增加了可用的相互作用数据,有助于药物重新定位和AI模型验证.
科学领域:
- 生物化学 生物化学
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 细胞功能依赖于小分子和蛋白质之间的相互作用.
- 化合物-蛋白质相互作用数据分散在不同的数据库中,格式不一致,阻碍了全面分析.
- 数据异质性对提取和整合实验约束性相互作用信息构成重大挑战.
研究的目的:
- 推出CPIExtract,这是一个用于交互式提取,过和协调化合物-蛋白相互作用数据的新工具.
- 克服数据异质性问题,提供化合物-蛋白相互作用的统一,丰富的数据集.
- 为了促进下游应用,如网络医学和机器学习模型开发.
主要方法:
- 开发CPIExtract,从多个化合物-蛋白质相互作用数据库中进行交互式数据提取.
- 实现过功能,以根据用户定义的标准来完善提取的数据.
- 将来自不同来源的数据协调成一个统一的格式.
主要成果:
- CPIExtract成功地提取和协调了实验性化合物-蛋白质相互作用数据.
- 该工具显示,与使用单个数据库 (如DrugBank) 相比,收集的注释数量增加了10倍以上.
- 输出数据可以通过过来定制并以标准的表格格式保存.
结论:
- CPIExtract提高了化合物-蛋白相互作用数据的可访问性和实用性.
- 该工具支持高级分析,包括用于药物重定向的网络医学和深度学习模型的交叉验证.
- CPIExtract为药理学和计算生物学研究人员提供了宝贵的资源.
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