PASSerRank:通过学习排名来预测全位点
Hao Tian1, Sian Xiao1, Xi Jiang2
1Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, USA.
一个新的学习排名 (LTR) 模型准确地识别了蛋白质中的全位,这对于药物发现至关重要. 这种计算方法显著改善了对这些重要的监管站点的预测.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 药理学 药理学是指药理学的学科.
背景情况:
- 体调节对蛋白质功能至关重要,也是药物开发中的一个关键目标.
- 识别异位是异药物发现的一个主要挑战.
- 现有的计算模型通常旨在在各种蛋白质家族中实现一般适用性.
研究的目的:
- 开发一种新的计算方法,用于准确预测全位.
- 利用学习排名 (LTR) 概念,根据它们的全性潜力对蛋白质口袋进行排名.
- 提供一个工具,帮助研究人员识别药物开发的潜在的全位.
主要方法:
- 实施一个学习排名 (LTR) 模型来优先考虑蛋白质口袋.
- 使用Allosteric数据库 (ASD) 和CASBench数据集对LTR模型进行培训和验证.
- 使用F1分数和马修斯相关系数等指标评估模型性能.
主要成果:
- LTR模型成功地将全囊在测试蛋白质的83.6% (ASD) 和80.5% (CASBench) 中排在前三名.
- 该模型与其他机器学习模型相比表现出更高的性能,获得更高的F1得分 (0.662 ASD,0.608 CASBench) 和马修斯相关系数 (0.645 ASD,0.589 CASBench).
结论:
- 开发的LTR模型提供了一个高度有效的计算策略,用于预测全位.
- 这种方法显著促进了全位的识别,促进了药物发现工作.
- 经过培训的模型可以通过PASSer平台访问,以支持正在进行的研究.
更多相关视频
06:50Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions
Published on: January 26, 2024
07:08Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
相关概念视频
Allosteric Proteins-ATCase
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Ligand Binding and Linkage
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Cooperative Allosteric Transitions
Predicting Reaction Outcomes
