Docking and MD Simulation of E6 Proteins in Complex with Sildenafil Ligand

The repository contains data from docking and molecular dynamics simulations of the HPV oncoproteins (E6 and E6AP) + Sildenafil ligand complex. E6, in conjunction with its associated ubiquitin ligase E6AP, are proteins encoded by high-risk Human Papillomavirus (HPVs), and sildenafil is a PDE-5 inhibitor ligand commonly used to treat erectile dysfunction. The objective is to see if sildenafil can be repurposed to inhibit the proteins, whether individually or in complex together, potentially blocking their ability to degrade the tumor suppressor protein p53, thereby supporting its utility in the treatment of HPV positive cervical cancer. The docking simulations were performed using Autodock Vina via AMDock The molecular dynamics simulations (200 ns simulation time) were performed using GROMACS via the BioExcel Building Blocks (biobb) interface The simulation data are divided into 3 archives: Docking+Simulation of E6-Sildenafil complex Docking+Simulation of E6AP-Sildenafil complex Docking+Simulation of E6+E6AP+Sildenafil complex. The Jupyter notebook used to post-process the data and extract information is also included