Persistent topology of protein space
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Publication:2080097
Abstract: Protein fold classification is a classic problem in structural biology and bioinformatics. We approach this problem using persistent homology. In particular, we use alpha shape filtrations to compare a topological representation of the data with a different representation that makes use of knot-theoretic ideas. We use the statistical method of Angle-based Joint and Individual Variation Explained (AJIVE) to understand similarities and differences between these representations.
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Cited in
(12)- Persistent similarity for biomolecular structure comparison
- Multiscale persistent functions for biomolecular structure characterization
- Biomolecular topology: modelling and analysis
- Atom-specific persistent homology and its application to protein flexibility analysis
- Evolutionary homology on coupled dynamical systems with applications to protein flexibility analysis
- A topological measurement of protein compressibility
- Using persistent homology and dynamical distances to analyze protein binding
- A topological approach for protein classification
- Topological linking and entanglement in proteins
- Protein classification with improved topological data analysis
- Bayesian topological learning for classifying the structure of biological networks
- A topology for the space of protein chains and a notion of local statistical stability for their three-dimensional structures
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