Examples of software that adopt the GUI type are SwissPDBviewer, Pymol, VMD, USCF Chimera, among others. Some examples of classic software that use CLI are Modeller for similarity modeling, Autodock for molecular docking and Gromacs for molecular dynamics. Structural Bioinformatics software most commonly uses CLI and GUI paradigms. These three paradigms currently co-exist depending on developers. Following the evolutionary cycle, the interface produced by the World Wide Web (or simply WEB) is considered as an evolution of GUIs. The first digital paradigm was the command line interfaces (CLI) followed by the evolution to the known graphical user interfaces (GUI). The paradigm of how software is executed has evolved as computing resources have improved. However, they continue with the same common implementation difficulties that plague researchers who are not computer specialists. Since its first versions, these softwares still remain as the most used and cited. More than three decades ago, the first MD softwares that were intended for biological problems were launched: Gromacs, AMBER and NAMD. Since its first applied approach to biology in 1977 much has evolved due to increased computational processing as well as improved coding. However, implementing a MD experiment is not trivial. The results obtained at the end of a MD are the richest and most complete in terms of non-quantum simulation. Furthermore, MD enables a wide range of studies, including molecular design (widely used in drug design), in determining structure and its refinement (X-ray, NMR and protein modeling). For example, macromolecular stability, identification of allosteric sites, elucidation of mechanisms of enzymatic activity, molecular recognition and properties of complexes with small molecules, association between proteins, protein folding and its hydration. ![]() With that, it is possible to obtain kinetic and thermodynamic characteristics of biomolecular structures. The Molecular Dynamics (MD) is one of the techniques incorporated into bioinformatics, specifically by structural bioinformatics. The code is freely available for download at GitHub. VisualDynamics was developed with Flask, which is a Python-based free and open-source framework for web development. Freely available at, is supported by all major web browsers. VisualDynamics is a tool that will accelerate implementations and learning in the area of molecular dynamics simulation. ![]() Can also download the graphics analysis and log files at the end of the simulation. In this new application the researcher can submit a simulation of the protein in the free form or complexed with a ligand. ![]() Here, we have developed the VisualDynamics-a WEB tool developed to automate biological simulations performed in Gromacs using a graphical interface to make molecular dynamics simulation user-friendly task. ![]() The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue with the same common implementation difficulties that plague researchers who are not computer specialists. The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures.
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