ArticleJournal of chemical information and modeling2023
VIAMD: a Software for Visual Interactive Analysis of Molecular Dynamics.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- From wireframes to immersive reality: a historical perspective on molecular visualization software.Briefings in bioinformatics · 2026Review
- De Novo Autogenic Engineered Living Functional Materials.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- From SMILES Codes for Reactants and Products to Transition States With VeloxChem.Journal of computational chemistry · 2026Article
- MOrbVis: Browser-Based Molecular Orbital Visualization with WebGPU-Accelerated On-the-Fly Evaluation.ACS omega · 2026Article
- MDNA : a software module for DNA structure generation and analysis.Nucleic acids research · 2026Article
- Molecular Dynamics Study of the Binding of Cationic, Anionic, and Neutral Luminescent Conjugated Ligands to the Alzheimer Folds of Aβ(1-42) and Tau Fibrils.Chembiochem : a European journal of chemical biology · 2026Article
- Multiphoton Absorption Spectra of Channelrhodopsin-2 via Multiscale Simulation Methods.Journal of chemical theory and computation · 2026Article
- VeloxChem: Large-Scale DFT Calculations of Geometric Derivatives up to Second Order for Simulation of IR Spectra.The journal of physical chemistry. A · 2026Article
- Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge.Journal of chemical information and modeling · 2026Article
- VeloxChem Quantum-Classical Interoperability for Modeling of Complex Molecular Systems.The journal of physical chemistry. A · 2025Article
- Molecular Shells and Range of Interactions in Ionic Liquids as a Function of Temperature.The journal of physical chemistry letters · 2025Article
- VeloxChem: GPU-Accelerated Fock Matrix Construction Enabling Complex Polarization Propagator Simulations of Circular Dichroism Spectra of G-Quadruplexes.The journal of physical chemistry. A · 2025Article
- Atomistic Simulations and Analysis of Peripheral Membrane Proteins with Model Lipid Bilayers.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Tuning the Emission of Bis-ethylenedioxythiophene-thiophenes upon Aggregation.The journal of physical chemistry. B · 2024Article
- Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments.International journal of molecular sciences · 2024Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 such as spatial distribution functions. VIAMD has the potential to advance research in many scientific disciplines and is a promising solution for improving the workflow of MD visualization and analysis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.