PDP-Miner:一种AI/ML工具,用于检测成千上万种细菌基因组中具有脱聚合酶域的益生菌尾蛋白
Jeff Gauthier1,2, Irena Kukavica-Ibrulj1,2, Roger C Levesque1,2
1Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
Bioinformatics (Oxford, England)
|August 21, 2025
概括
菌体尾部蛋白质是抗生素的一个有希望的替代品. 在Pseudomonas基因组中识别潜在的脱聚酶基因,帮助对抗抗生素耐药性.
科学领域:
- 微生物学
- 生物信息学
- 基因组学
背景情况:
- 抗生素耐药性是一个日益严重的全球健康危机, 自1987年以来,
- 菌体尾蛋白,特别是针对细菌外膜多糖的脱聚酶,代表了一个有前途的替代治疗策略.
- 病原细菌常常含有菌体,为菌体衍生疗法提供已知的分子点.
研究的目的:
- 开发一种用于识别体脱聚酶基因的计算工具.
- 在菌体尾蛋白中注释和检测脱聚酶活性.
- 通过分析蛋白质域来验证潜在的脱聚合酶候选物.
主要方法:
- 开发了PDP-Miner,这是基于机器学习的Depolymerase-Predictor工具的封装.
- 标注的菌体尾巴蛋白和检测到的脱聚酶活性.
- 通过对脱聚酶指标的蛋白质域进行后期验证.
主要成果:
- 鉴定了来自国际伪omonas联盟数据库的1294个伪omonas基因组中的10个高可信度的菌体脱聚合酶基因候选物.
- 在已知的菌体基因组中准确地报告了脱聚酶.
- 与现有工具如PhageDPO和DepoScope具有相似的性能.
结论:
- PDP-Miner是一种有效的工具,用于识别新菌体脱聚合酶候选物.
- 该工具有助于发现抗生素耐药性的潜在抗菌剂.
- 促进治疗应用的菌体蛋白质的研究.
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