MOanalys

MOanalys is an open-source tool designed for the analysis of molecular dynamics (MD) simulations, particularly those generated using the GROMACS molecular dynamics software package. Developed as a Python-based application, MOanalys provides users with a user-friendly interface to visualize and interpret complex simulation data, making it accessible to both experts and researchers new to MD analysis.

The software focuses on several key functionalities, including the calculation of structural properties such as root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), and hydrogen bond analysis. It also supports the generation of contact maps, which help in studying protein folding and interactions. Additionally, MOanalys can compute secondary structure elements, such as alpha-helices and beta-sheets, using algorithms like DSSP (Define Secondary Structure of Proteins).

One of its notable features is the ability to perform principal component analysis (PCA) and essential dynamics analysis, which are useful for identifying collective motions in biomolecular systems. MOanalys integrates with GROMACS through its compatibility with standard trajectory and topology file formats, ensuring seamless workflow integration. The tool also includes visualization capabilities, allowing users to overlay structural data on molecular models for better interpretation.

MOanalys is distributed under an open-source license, encouraging collaboration and customization. It is particularly useful for researchers in computational biology, biophysics, and structural biology who rely on MD simulations to study molecular behavior. The software is continuously updated to incorporate new analysis methods and improvements based on user feedback.