Fig. 1

Schematic representation of COMMA workflow. Starting from one or several MD trajectories, COMMA computes matrices of residue-based dynamic properties: local dynamical correlations (Corr ^L F A ), minimum distances (Dist), communication propensities (CP), non-covalent interaction strengths (INT) and secondary structures (SS). Local dynamical correlations and minimum distances are used to identify independent cliques while communication propensities, non-covalent interaction strengths and secondary structures are used for communication pathway detection. A coloured graph, called Protein Communication Network (PCN), is constructed from independent cliques (blue edges) and communication pathways (red edges). The graph is analysed and two groups of communication blocks are extracted. The first group is made of clique-based blocks (blue cliques in PCN), and the second group is made of pathway-based blocks (subgraphs of the red PCN) where pathways have bounded length. In the schema, three different pathway-based blocks are displayed, corresponding to a minimal path length of 4 (red), 8 (orange) and 9 (yellow) respectively. Communication pathways are also used to detect pairs of communicating segments, which are portions of secondary structure elements. Residues belonging to pathways that cross two secondary structures are coloured. For each pair of segments, the communication strength of the interaction is evaluated, on a scale of strengths going from low (pink) to strong (violet) strength. The segments and their interaction strength between H1-H2, H1-H3 and H2-H3 helices are shown