Molecular dynamics simulations of proteins: A multi-phase pipeline for protein modeling

Running molecular dynamics simulations of proteins is a major necessity for computational biologists to understand diseases and design therapies. However, these simulations require massive and expensive computational resources to obtain vital biological results. This is the key restrictive factor in the computational biology field, and to reduce this restriction, researchers must resort to supercomputers. In this work, we present a pipeline to run computational simulations of proteins using high-performance computing resources, initiating from the retrieval of protein amino acid sequences to job submission on supercomputers. We show the pipeline in execution by characterizing, modeling, preparing, and simulating a viral protein and a bacterial species protein.