GUI-BioPASED: A program for molecular dynamics simulations of biopolymers with a graphical user interface

Abstract

There are several software packages that allow the user to model main types of biopolymers with molecular dynamics methods. However, the work with most of these packages is quite complicated, especially for non-experts in computational structural biology. We have created GUI-BioPASED, a Web-based GUI for molecular dynamics software BioPASED, to partially automate the tasks usually responsible for the majority of errors. GUI-BioPASED creates a task as a standalone executable file, which can be exported to the client side, and ensures its execution. A user-friendly cross-platform interface is created that performs data check, reports errors and hints at possible ways to correct them. BioPASED, a general purpose molecular dynamics program, and GUI-BioPASED along with their typical example of usage are described.