MD-ligand-receptor software

MD-ligand-receptor is a bioinformatics pipeline written in  Python for analyzing non-covalent ligand-receptor interactions in 3D  structures starting from a molecular dynamic trajectory.
Through GROMACS, the trajectory is divided into single timestamps that are analyzed by PLIP (Protein-Ligand Interaction Profiler);  the end results are CSV and JSON files containing all the non-covalent  interactions between the protein and ligand, each labeled with its  trajectory timestamp. In order to better visualize and organize the output data, we offer a  plotly dashboard  which provide a series of interactive plots.

The Python pipeline is designed for use within either a  multicore linux server or a multi-node HPC cluster with the  implementation of MPI for Python; data parallelism is necessary for the heavy computation needed to partition and analyze the trajectory data.
The following figure shows an high level overview of the Software's  pipeline. The software take as input a .xtc and .tpr file, divide the  workload for parallel computing, will then produce .pdb files which are  analyzed by plip, the results are then merged into json and csv files,  ready to be visualized.

visit the github page (https://github.com/fraMade/MD_ligand_receptor) for more informations.