ASGARD. A simple and automatic GROMACS tool to analyze Molecular Dynamic simulations

Abstract

One of the most featured techniques to analyze the physical movement of molecules is Molecular Dynamics (MD) simulations. Among the different programs used to perform them, GROMACS is one of the most widely used open-source packages. We present ASGARD, a software to perform analysis of MD protein or protein-ligand complex simulations and to generate the corresponding report via an automated MD workflow. This tool automatically generates a set of analyses after completing the simulation, including reports about overall system stability and system flexibility analysis with RMSD Fluctuation and Distribution calculations. Finally, a dynamic analysis with SASA and DSSP method graphs, and different interaction analyses are performed. In conclusion, ASGARD allows the user to run MD simulation analysis with a single command line instead of using the GROMACS programs individually. Following this, it automatically creates an analysis report which helps to understand the molecular interactions and structural changes.

In silico discovery of potential sodium–glucose cotransporter-2 inhibitors from natural products for Prevent Kidney Failure in Patients with Type 2 Diabetes

“…The pharmacokinetic properties of the six desired compounds were investigated along with the standard drug empagli ozin and three approved drugs (canagli ozin, dapagli ozin, and ertugli ozin) using programs the Schrödinger (Schrodinger Release 2021.2: QikProp, Schrodinger, LLC, New York, NY, 2021) and SwissADME [44][45][46][47] , that only two compounds (306 and 580) were in range for 95% known drugs. After examining the docking studies of the two selected compounds of the previous stage and the approved drugs utilizing Moe 2019 48,49 , a proper conformer of the standard drug and compounds 306, and 580 was entered into a molecular simulation study via GROMACS 2018 50,51 . Then, the prediction of cytochrome P450 mediated metabolism for the three said compounds with the use of the SMARTCyp online server 52,53 was investigated.…”