MD-Ligand-Receptor: a HPC tool for characterizing ligand receptor binding interactions in molecular dynamics trajectories

 We present MD-Ligand-Receptor, an efficient high-performance structural bioinformatics pipeline for the analysis of  ligand-receptor binding interactions  as a function of time, obtained from the analysis of molecular dynamics trajectories. The pipeline has been developed to work on a multicore linux server as well as on a multi-node HPC cluster. In the latter case,  MD-Ligand-Receptor allows the user to analyze large trajectories in a very short time. In addition, an easy-to-use Plotly dashboard is provided to view the results of the interaction in several graphical ways. 

The three folders contain:

test_data: a molecular dynamics trajectory of 100K picoseconds and the corresponding  system topology. This input data can be used to test the software.

result_data: the results obtained by running the software on the test data. The result files are ready to be visualized in a Plotly dashboard, as described in the GitHub repository.

MD_ligand_receptor_software: the whole software as reported in the GitHub repository.

Authors:  [Francesco Madeddu, Michele Pieroni, Jessica Di Martino, Manuel Arcieri, Valerio Parisi, Paolo Bottoni and Tiziana Castrignanò]