BMC Bioinformatics | |
Detecting intermediate protein conformations using algebraic topology | |
Research | |
Dong Luo1  Nurit Haspel1  Eduardo González2  | |
[1] Department of Computer Science, University of Massachusetts Boston, 100 Morrissey Blvd., 02125, Boston, MA, USA;Department of Mathematics, University of Massachusetts Boston, 100 Morrissey Blvd., 02125, Boston, MA, USA; | |
关键词: Algebraic topology; Protein conformational sampling; Clustering; Protein structure; Dimensionality reduction; | |
DOI : 10.1186/s12859-017-1918-z | |
来源: Springer | |
【 摘 要 】
BackgroundUnderstanding protein structure and dynamics is essential for understanding their function. This is a challenging task due to the high complexity of the conformational landscapes of proteins and their rugged energy levels. In particular, it is important to detect highly populated regions which could correspond to intermediate structures or local minima.ResultsWe present a hierarchical clustering and algebraic topology based method that detects regions of interest in protein conformational space. The method is based on several techniques. We use coarse grained protein conformational search, efficient robust dimensionality reduction and topological analysis via persistent homology as the main tools. We use two dimensionality reduction methods as well, robust Principal Component Analysis (PCA) and Isomap, to generate a reduced representation of the data while preserving most of the variance in the data.ConclusionsOur hierarchical clustering method was able to produce compact, well separated clusters for all the tested examples.
【 授权许可】
CC BY
© The Author(s) 2017
【 预 览 】
Files | Size | Format | View |
---|---|---|---|
RO202311090538027ZK.pdf | 2023KB | download | |
12864_2017_3492_Article_IEq14.gif | 1KB | Image | download |
12864_2017_3487_Article_IEq2.gif | 1KB | Image | download |
12864_2017_3492_Article_IEq16.gif | 1KB | Image | download |
12864_2017_3605_Article_IEq19.gif | 1KB | Image | download |
12864_2017_3492_Article_IEq17.gif | 1KB | Image | download |
12864_2017_3609_Article_IEq14.gif | 1KB | Image | download |
12864_2017_4269_Article_IEq2.gif | 1KB | Image | download |
【 图 表 】
12864_2017_4269_Article_IEq2.gif
12864_2017_3609_Article_IEq14.gif
12864_2017_3492_Article_IEq17.gif
12864_2017_3605_Article_IEq19.gif
12864_2017_3492_Article_IEq16.gif
12864_2017_3487_Article_IEq2.gif
12864_2017_3492_Article_IEq14.gif
【 参考文献 】
- [1]
- [2]
- [3]
- [4]
- [5]
- [6]
- [7]
- [8]
- [9]
- [10]
- [11]
- [12]
- [13]
- [14]
- [15]
- [16]
- [17]
- [18]
- [19]
- [20]
- [21]
- [22]
- [23]
- [24]
- [25]
- [26]
- [27]
- [28]
- [29]
- [30]
- [31]
- [32]
- [33]