SpecP: A tool for spectral partitioning of protein contact graph.

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.

Looking for a sequence based allostery definition: a statistical journey at different resolution scales.

The aim of this work was to detect allosteric hotspots signatures characterizing protein regions acting as the 'key drivers' of global allosteric conformational change. We computationally estimated the relative strength of intra-molecular interaction in allosteric proteins between two putative allostery-susceptible sites using a co-evolution model based upon the optimization of the cross-correlation in terms of free-energy-transfer hydrophobicity scale (Tanford scale) distribution along the chain. Cross-Recurrence Quantification Analysis (Cross-RQA) applied on the sequences of allostery susceptible sites showed evidence of strong interaction amongst allosteric susceptible sites.

Sequence signatures of allosteric proteins towards rational design.

Allostery is the phenomenon of changes in the structure and activity of proteins that appear as a consequence of ligand binding at sites other than the active site. Studying mechanistic basis of allostery leading to protein design with predetermined functional endpoints is an important unmet need of synthetic biology. Here, we screened the amino acid sequence landscape in search of sequence-signatures of allostery using Recurrence Quantitative Analysis (RQA) method.