Extracting Dynamical Correlations and Identifying Key Residues for Allosteric Communication in Proteins by correlationplus

Extracting dynamical pairwise correlations and identifying key residues from large molecular dynamics trajectories or normal-mode analysis of coarse-grained models are important for explaining various processes like ligand binding, mutational effects, and long-distance interactions. Efficient and flexible tools to perform this task can provide new insights about residues involved in allosteric regulation and protein function. In addition, combining and comparing dynamical coupling information with sequence coevolution data can help to understand better protein function. To this aim, we developed a Python package called correlationplus to calculate, visualize, and analyze pairwise correlations. In this way, the package aids to identify key residues and interactions in proteins. The source code of correlationplus is available under LGPL version 3 at https://github.com/tekpinar/correlationplus. The current version of the package (0.2.0) can be installed with common installation methods like conda or pip in addition to source code installation. Moreover, docker images are also available for usage of the code without installation.

Automated summary

The Python package correlationplus is developed to extract dynamical pairwise correlations from large molecular dynamics trajectories or normal-mode analysis, identifying key residues and interactions in proteins. By combining dynamical coupling information with sequence coevolution data, it provides new insights about protein function and aids in better understanding of residues involved in allosteric regulation. The package can be easily installed with common methods like conda or pip, and docker images are also available for usage without installation.