Antibody-SARS-CoV-2-Molecular-Dynamics-setup-and-energy-estimation

This tutorial aims to illustrate the process of setting up a simulation system containing an antibody and a SARS-CoV-2 protein, step by step, using the SWISS-MODEL, VMD and NAMD. The energy estimation is implemented using AutoDock Tools, scripts with commands are provided.
File Tutorial.ipynb containes detailed tutorial. Minimized input files are in the folder 'Input structures'. The part Validation of SARS-AB on an independent dataset without crystal structures was implemented on a dataset 'Input structures/Dataset_without_crystal_structures'. The Regdanvimab analogs are in the folder 'Input structures/Regdanvimab'.