Communication pathway analysis within protein-nucleic acid complexes

We developed ComPASS, a large-scale computational method designed to study communication networks in protein-protein and protein-nucleic acid complexes. Recognizing the significance of dynamics in the communication of macromolecules, our approach leverages molecular dynamics (MD) simulation data to extract inter-residue key properties, including dynamical correlations, interactions, and distances. These properties are integrated to construct a weighted communication network that comprehensively represents dependencies among amino acids and nucleotides. Using ComPASS, we uncovered distinct mechanisms of signal transmission in diverse macromolecular systems, namely Cysteinyl-tRNA synthetase (1u0b), LacI repressor, Type IIF restriction endonuclease Bse634I, liver X receptor, and four nucleosome complexes (1kx5, 1kx5_L1, 1f66, ncp601). Here we share the MD trajectories for each system, as well as the ComPASS results.