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本仓库收录了人乳头瘤病毒（Human Papillomavirus, HPV）致癌蛋白（E6与E6AP）与西地那非配体所形成复合物的分子对接及分子动力学模拟数据。E6与其关联的泛素连接酶E6AP均由高危型人乳头瘤病毒（HPVs）编码，而西地那非是一种常用于治疗勃起功能障碍的PDE-5抑制剂配体。本研究旨在探究西地那非是否可被老药新用，以单独存在或形成复合物的形式抑制上述蛋白，潜在阻断其降解肿瘤抑制蛋白p53的能力，进而为其在HPV阳性宫颈癌治疗中的应用提供支持。 分子对接模拟采用Autodock Vina工具，通过AMDock接口完成。 时长为200 ns的分子动力学模拟则通过GROMACS工具，借助BioExcel构建模块（BioExcel Building Blocks, biobb）界面完成。 本模拟数据分为3个归档文件： 1. E6-西地那非复合物对接与模拟数据集 2. E6AP-西地那非复合物对接与模拟数据集 3. E6+E6AP+西地那非复合物对接与模拟数据集 本仓库同时附带用于数据后处理与信息提取的Jupyter笔记本文件。