Abstract
SpecP is an open-source Python module that performs Spectral Partitioning on Protein Contact Graphs. Protein Contact Graphs are graph theory based representation of the protein structure, where each amino acid forms a ‘vertex’ and spatial contact of any two amino acids is an ‘edge’ between them. Spectral partitioning is carried out in SpecP based on the second smallest spectral value (eigen value) of the Protein Contact Graph. The eigen vector corresponding to the second smallest spectral value are partitioned into two clusters based on the sign of the corresponding vector entry. Spectral Partitioning algorithm is repeatedly carried out until the desired numbers of partitions are obtained. SpecP visualizes the spectrally partitioned clusters of protein structure along with the Protein Contact Map and Protein Contact Graph which can be saved for later use. It also possesses an interactive mode whereby the user has the ability to zoom, pan, resize and save these raster images in various image formats (.eps, .jpg, .png) manually. SpecP is a stand-alone extensible tool useful for structural analysis of proteins.
Highlights
Spectral partitioning is a graph partition algorithm which partitions data represented in the form of a graph G = (V,E), with V vertices and E edges, into smaller components with specific properties [1]
Proteins are depicted as graph with the amino acids as nodes and the positional information of the Cα atoms that form the backbone of protein structure, as edge connectivity or ‘contact’
A contact map or adjacency matrix is a square matrix M where Mi,j=1 if the distance between Cα atoms of residues i and j is below cut-off threshold atomic distance, or Mi,j=0 otherwise
Summary
Proteins are depicted as graph with the amino acids as nodes and the positional information of the Cα atoms that form the backbone of protein structure, as edge connectivity or ‘contact’. The Protein Contact Graph of the first 10 nodes for the protein (PDB id 4q21) is as shown in (Figure 1). The Spectral Partitioning algorithm is applied on the Protein Contact Map obtained from Protein Contact Graph.
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