基于使用卷积神经网络的蛋白质序列的多重histidine后翻译修饰 (PTM) 预测服务器:对质谱数据的案例研究
Dibyansu Diptiman1, Abhishek Jalan1, Rishabh Pal1
1Department of Biological Sciences, Birla Institute of Technology and Science, Hyderabad, India.
这项研究介绍了Hist-i-fy,Hist-i-fy是一种用于预测蛋白质多个histidine后翻译修饰 (PTMs) 的新型计算工具. 它在现有的单一功能预测器上提供了显著的进步,有助于表征具有未知功能的蛋白质.
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:
- 丁后翻译修饰 (PTMs) 对酶功能至关重要,但在实验上具有挑战性.
- 对于Histidine-PTM预测的现有计算工具是有限的,通常只能预测单个修改类型.
- 未知功能的蛋白质 (PUF) 和未知功能的域 (DUF) 需要高效的表征方法.
研究的目的:
- 开发和验证一种用于预测多个histidine-PTM类型的新型计算工具.
- 为了解决现有的单一功能胺-PTM预测工具的局限性.
- 为了促进蛋白质的功能注释,特别是PUF和DUF.
主要方法:
- 从UniProt数据库 (n=1584) 整理了一组功能性歇斯蒂丁修饰的数据集.
- 采用人工神经网络,特别是一个名为"Hist-i-fy"的卷积神经网络 (CNN) 模型.
- 使用质谱数据验证了对丁酸化 (n=34) 的模型.
主要成果:
- "Hist-i-fy"CNN模型实现了75%的整体准确性和F1得分.
- 该工具成功地预测了八种不同的histidine功能:乙化,利化,糖化,化,甲基化,氧化,化和蛋白质拼接.
- 一个关于histidine-phosphorylation的案例研究表明了该工具的有效性.
结论:
- "Hist-i-fy"代表了第一个具有最佳性能的多重Histidine-PTM预测工具.
- 这种工具有助于对酶活性位点和蛋白质功能的计算表征.
- 开发的工具是公开的,促进更广泛的研究应用.
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