GradPose:一个非常快速和存储效率高的梯度下降工具,用于从计算模拟中叠加数百万个蛋白质结构
Daniel T Rademaker1, Kevin J van Geemen1, Li C Xue1
1Department of Medical BioSciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.
Bioinformatics (Oxford, England)
|July 20, 2023
概括
GradPose 是一种用于快速和存储效率高的蛋白质结构叠加的新工具,在通过计算模拟生成的大数据集的传统方法中显著优于传统方法.
科学领域:
- 计算生物学是一种计算生物学.
- 结构生物信息学 结构生物信息学
背景情况:
- 像分子动力学和对接这样的计算模拟产生了大量的蛋白质构造.
- 分析这些大型数据集需要有效的结构比较和集群方法.
- 现有的结构叠加方法可能是计算密集型和内存密集型.
研究的目的:
- 介绍GradPose,这是一个用于快速和记忆效率高的结构叠加的新工具.
- 解决对大规模蛋白质模拟数据有效分析的需求.
- 为蛋白质结构的最佳叠加提供解决方案,包括处理插入和删除.
主要方法:
- 使用旋转四次子的梯度下降优化用于结构叠加.
- 设计以提高记忆效率,并可扩展到数百万种蛋白质结构.
- 利用多核CPU处理和可选的CUDA加速来提高速度.
- 需要预先确定的残留物-残留物对应.
主要成果:
- 与传统方法相比,GradPose显示了显著的速度改进 (2-65倍) 和内存减少 (1.7-48倍).
- 较大的蛋白质结构从GradPose的效率中受益最多.
- 传统的方法仅对非常小的蛋白质 (约. 20个残留物).
结论:
- 在计算模拟中,GradPose为结构对齐提供了一个计算效率高的解决方案.
- 该工具有效地处理大量的蛋白质构造数据集.
- GradPose 增强了蛋白质动态和相互作用形状的分析.
相关概念视频
Protein Complexes with Interchangeable Parts
2.6K
Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...
2.6K
Protein and Protein Structures
10.6K
10.6K
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
Protein Complex Assembly
2.1K
2.1K
Protein and Protein Structure
79.8K
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...
79.8K


