biostudies-literatureUnknown63(23)Skanberg RKnut och Alice Wallenbergs StiftelseSwedish e-Science Research CentreThe typical workflow in molecular dynamics (MD) analysis requires several separate tools, often resulting in a lack of synergy and interaction between the individual analysis steps. This article presents VIAMD, an application designed to address this issue by integrating a 3D visualization of molecular trajectories with flexible analysis components. VIAMD uses an interactive scripting interface, allowing for property definition and evaluation. The application provides context-aware suggestions and expression feedback through information and visualizations. The user-defined properties can be explored and analyzed through the various components. This enables correlation with spatial conformations, statistical analysis of distributions, and powerful aggregation of multidimensional properties Journal of chemical information and modeling7382-7391https://www.ebi.ac.uk/biostudies/studies/S-EPMC10716899biostudies-literatureVIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics.PMC10716899Skanberg RLinares MHotz IYnnerman AfalseVIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics.The typical workflow in molecular dynamics (MD) analysis requires several separate tools, often resulting in a lack of synergy and interaction between the individual analysis steps. This article presents VIAMD, an application designed to address this issue by integrating a 3D visualization of molecular trajectories with flexible analysis components. VIAMD uses an interactive scripting interface, allowing for property definition and evaluation. The application provides context-aware suggestions and expression feedback through information and visualizations. The user-defined properties can be explored and analyzed through the various components. This enables correlation with spatial conformations, statistical analysis of distributions, and powerful aggregation of multidimensional properties 2023-01-01T00:00:00Z2023 Dec2026-05-28T15:35:58.07Z2025-04-04T21:21:13.963ZS-EPMC107168993801102610.1021/acs.jcim.3c01033