ProteinGym:用于蛋白质设计和健身预测的大规模基准
Pascal Notin1, Aaron W Kollasch2, Daniel Ritter2
1Computer Science, University of Oxford.
bioRxiv : the preprint server for biology
|December 18, 2023
概括
ProteinGym提供了一个大规模的基准,用于评估蛋白质适应性预测和设计中的机器学习模型. 本资源旨在标准化对各种蛋白质家族和实验数据的评估,改进用于卫生和农业应用的模型开发.
科学领域:
- 计算生物学 计算生物学
- 蛋白质工程是指蛋白质工程.
- 机器学习 机器学习
背景情况:
- 预测蛋白质突变效应对于理解遗传疾病和设计用于气候,农业和医疗保健的新型蛋白质至关重要.
- 目前用于蛋白质分析的机器学习模型面临着挑战,原因是各种数据集和蛋白质家族之间的不一致性能.
研究的目的:
- 介绍ProteinGym,这是一个全面的基准套件,用于大规模的蛋白质健身预测和设计.
- 在蛋白质领域标准化机器学习模型的评估.
主要方法:
- 开发了ProteinGym,结合了250多个深度突变扫描试验和策划的临床数据集.
- 创建了一个强大的评估框架,评估适应性预测和设计能力,考虑到实验限制.
- 在零射击和监督环境中评估了70多种不同的机器学习模型.
主要成果:
- ProteinGym提供了一个统一的基准来比较各种蛋白质模型类型,包括基于对齐和反向折叠的方法.
- 适应性预测和设计的性能指标在广泛的蛋白质家族中得到了标准化.
- 该研究系统地评估和比较了众多现有模型的性能.
结论:
- ProteinGym提供了一个可扩展和整体的解决方案,用于对蛋白质健身预测和设计模型进行基准测试.
- 开源代码库,数据集和用户友好的网站促进了蛋白质工程的更广泛的研究和开发.
- 标准化评估对于在蛋白质科学中推进机器学习应用至关重要.
相关概念视频
02:04Protein-protein Interfaces
12.5K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.5K
01:49Conserved Binding Sites
4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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...
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...
4.2K
02:26Protein Networks
4.0K
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,...
4.0K
02:47Protein Families
15.4K
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...
15.4K