Machine Learnable Fold Space Representation based on Residue Cluster Classes
- PMID: 26366526
- DOI: 10.1016/j.compbiolchem.2015.07.010
Machine Learnable Fold Space Representation based on Residue Cluster Classes
Abstract
Motivation: Protein fold space is a conceptual framework where all possible protein folds exist and ideas about protein structure, function and evolution may be analyzed. Classification of protein folds in this space is commonly achieved by using similarity indexes and/or machine learning approaches, each with different limitations.
Results: We propose a method for constructing a compact vector space model of protein fold space by representing each protein structure by its residues local contacts. We developed an efficient method to statistically test for the separability of points in a space and showed that our protein fold space representation is learnable by any machine-learning algorithm.
Availability: An API is freely available at https://code.google.com/p/pyrcc/.
Copyright © 2015 Elsevier Ltd. All rights reserved.
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