在MODELLER中使用平均方法来预测蛋白质结构
Serena Rosignoli1, Elisa Lustrino1, Iris Di Silverio1
1Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy.
International journal of molecular sciences
|February 10, 2024
概括
本研究介绍了MODELLER的平均化技术.
科学领域:
- 计算生物学 计算生物学
- 结构生物信息学 结构生物信息学
- 蛋白质建模模型
背景情况:
- 像AlphaFold 2这样的高级蛋白质结构预测方法在静态结构方面表现出色,但在动态特征方面扎.
- 基于同质学的建模为蛋白质结构预测提供了具有成本效益的替代方案.
- 在模拟化过程中,MODELLER算法生成中间模型,探索构造状态.
研究的目的:
- 调查中介模型的平均值是否能提高结构质量.
- 评估统计潜力排名对选择最佳模型的有效性.
- 探索单个与多个模板对平均方法的影响.
- 为了确定MODELLER的合奏相能否捕捉低能量的全息形状.
主要方法:
- 使用MODELLER (版本10.5) 检查了225个目标模板对.
- 根据统计潜力提取和平均的代表性中间模型.
- 评估模型质量改进和排名可靠性.
主要成果:
- 通过对中间模型进行平均化,在结构上与本地结构的相似性方面取得了轻微但显著的改进.
- 平均化程序在低序列同一性区域和全蛋白形态生成中特别有益.
- 很大一部分平均配置的相似性高于MODELLER的最终输出.
结论:
- 平均介质MODELLER模型可以提高结构模型的质量,特别是在具有挑战性的同质模型场景中.
- 统计潜力排名有助于选择改进的模型.
- 该方法在捕获全蛋白形状方面表现有前途,这是传统方法经常缺陷的领域.
相关概念视频
Protein and Protein Structure
79.5K
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme...
A protein's shape is critical to its function. For example, an enzyme...
79.5K
Protein and Protein Structures
10.5K
10.5K
Protein Folding Quality Check in the RER
3.7K
ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
3.7K
Conservation of Protein Domains Over Different Proteins
10.9K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.9K
Predicting Molecular Geometry
34.3K
VSEPR Theory for Determination of Electron Pair Geometries
34.3K
Molecular Models
38.4K
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.
38.4K


