图形MHC:新抗原预测模型,将图形神经网络应用于分子结构
Hoyeon Jeong1, Young-Rae Cho2, Jungsoo Gim3
1Department of Biostatistics, Yonsei University, Wonju, Gangwon State, Republic of Korea.
PloS one
|March 27, 2024
概括
一种新的图形神经网络模型GraphMHC准确地预测了新抗原与MHC蛋白质的结合. 这种方法提高了癌症患者对免疫检查点抑制剂的预后预测.
科学领域:
- 计算生物学是一种计算生物学.
- 免疫信息学是指免疫信息学.
- 癌症研究 癌症研究
背景情况:
- 新抗原是预测患者对免疫检查点抑制反应的关键生物标志物.
- 目前使用深度神经网络的预测模型对于生物分子相互作用缺乏解释性.
- 对新抗原-MHC结合的准确预测对于个性化癌症治疗至关重要.
研究的目的:
- 开发一个可解释的图形神经网络模型,GraphMHC,用于模拟新抗原-MHC蛋白结合.
- 提高预测新抗原结合亲和力的准确性及其临床相关性.
- 为癌症免疫学中模拟生物分子相互作用提供一个特征内在的方法.
主要方法:
- 利用图形神经网络 (GNN) 来模拟来自免疫表皮层数据库 (IEDB) 的氨基酸序列的分子结构.
- 将氨基酸序列转换为图形表示,捕获原子信息和原子间连接.
- 采用堆叠图的注意力和卷积层进行绑定分类.
主要成果:
- GraphMHC实现了高预测性能,接收器操作特征曲线 (AUC) 下的面积为92.2%.
- 该模型在准确性方面超过了基线预测模型.
- 应用到癌症基因组图谱 (TCGA) 黑色素瘤数据显示,高和低新抗原负载组之间的肌体得分和总生存率的边界差异存在显著差异,这是基线模型错过的区别.
结论:
- GraphMHC提供了第一个基于GNN的特征内在方法,用于使用分子结构建模新抗原-MHC结合.
- 该模型提供了对新抗原结合的高度准确,可解释的见解.
- GraphMHC有可能显著改善接受免疫检查点抑制剂治疗的癌症患者的预后预测.
相关概念视频
02:00Molecular Models
38.3K
Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.
38.3K
02:26Protein Networks
3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K
02:27Predicting Molecular Geometry
34.3K
VSEPR Theory for Determination of Electron Pair Geometries
34.3K
02:40Ligand Binding Sites
12.8K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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...
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...
12.8K