X-Pro: A web-based tool to analyze the loss and gain of local interaction upon a point mutation on protein structures

Understanding how point mutations affect protein structures is critical for understanding their impacts on a protein’s function and, eventually their role in causing diseases or biological differences. In recent decades, structural inferences of missense mutations have gained significant attention due to their importance in understanding monogenic disorders. Making point mutations in silico is one of the simple bioinformatics tasks. Existing GUI-based open-source tools like PyMOL, Chimera, Discovery Studio, etc., have simplified this task so that it can be done with a few mouse clicks. However, this continues to be a difficult task for untrained biologists. Further, understanding the loss and gain of interactions caused by such mutations remains even more challenging to them. To address this, we have developed a simple web-browser-based application named X-Pro wherein a PDB structure, chain ID, residue number, and the target mutation are taken as inputs, along with mutation information. The tool runs PyMOL and LigPlot tools in the back-end, taking the site of mutation as the ligand and returning graphical images of the structure before and after in-silico point mutation, and a table listing the loss and gain of interactions arising from this mutation. The tool is available for users at the URL http://bts.ibab.ac.in/X-Pro.php .