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Quacking Dynamics
Advanced Molecular Dynamics & Docking Visualization Platform.
Powered by Amber99sb-ildn and AutoDock Vina.
Explore complex protein structures with our high-performance NGL.js engine. Smooth, interactive, and scientifically accurate.
Visualize ligand binding in real-time. Analyze interactions, pockets, and surface properties with intuitive controls.
Take your research to the next level. Export your results to VR-ready formats and explore the molecular world from within.
Set a fixed value to reproduce the exact same docking pose.
| Pose | Affinity | RMSD lb | RMSD ub |
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Generates GROMACS simulation pipeline (main_md.sh) for the selected docked pose and VR files.
| Verified | Active | Admin | Experiments | Registered | Actions | |
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The selected ligand contains multiple disconnected fragments or conformations. Proceeding with all of them may cause docking errors.
Please select the fragment you want to keep:
The selected PDB file contains multiple NMR models. AutoDock Vina and MD simulations require a single structural model.
Please select the model you want to keep:
Last updated: May 2026 — RePoSUDOE Project
By accessing or using this platform, you agree to these Terms of Use. If you do not agree, please discontinue use immediately.
This platform is intended exclusively for academic, scientific, and non-commercial research purposes in the field of computational biochemistry. You may use this service to:
You may not:
You are solely responsible for the files you upload. Do not upload confidential, proprietary, or personally identifiable data. The platform does not guarantee the confidentiality of uploaded molecular structures beyond the security measures described in the Privacy Policy.
All computational results (docking scores, binding poses, MD trajectories, analysis reports) are provided for research guidance only. They do not constitute clinical, pharmaceutical, or regulatory advice. The platform and its operators make no warranty, express or implied, regarding the accuracy, completeness, or fitness for any particular purpose of the results.
To the fullest extent permitted by law, the RePoSUDOE consortium and its partner institutions shall not be liable for any direct, indirect, incidental, or consequential damages arising from the use of or inability to use this platform or its results.
If you publish results obtained using this platform, we ask that you acknowledge the RePoSUDOE project and cite the relevant software tools used (AutoDock Vina, GROMACS, etc.) according to their respective citation requirements.
These terms may be updated periodically. Continued use of the platform after changes are posted constitutes acceptance of the revised terms.
Last updated: May 2026 — RePoSUDOE Project
This platform is developed and operated within the RePoSUDOE project, a collaborative research initiative funded by the Interreg SUDOE Programme (European Regional Development Fund). Partner institutions include USC, MDUSE, IPG, UDC, CITIC, CNRS, CBMN, SPSP, and CSG.
When you use this platform, the following data may be processed:
Uploaded files and results are processed exclusively to perform the requested computational analysis (molecular docking and/or molecular dynamics simulation). Data is not used for any commercial purpose, sold to third parties, or shared outside the project consortium.
Experiment data is retained on the server for the duration necessary to complete the analysis and allow result download. Users may delete their experiments at any time via the Dashboard. Server logs are retained for a maximum of 90 days.
Processing is carried out on the basis of legitimate interests (Article 6(1)(f) GDPR) for the provision of the research service, and consent (Article 6(1)(a) GDPR) for account registration. Users located in the European Economic Area have the right to access, rectify, erase, and port their personal data.
We implement technical and organisational measures to protect uploaded data and account information. Uploaded molecular files are stored in isolated per-experiment directories and are not publicly accessible.
For any privacy-related request or inquiry, please contact the RePoSUDOE project team through the official project channels at the partner institutions listed above.
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