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BioSim (Biomolecular Simulations) Data Resources

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BioSimDR logo

BioSimDR (Biomolecular Simulation Data Resources) is a collection of tools and data services designed to transform and store biomolecular simulations by capturing and archiving the full provenance of each simulation. Our tools can be used to meticulously record every step - from experimental structures to force field configurations and computational parameters - ensuring research is reproducible, transparent, and efficient. Our data services allow for biomolecular simulations to be stored, shared, and discovered in one place. This approach helps scientists to avoid redundant efforts, improves the reliability of findings, and supports AI-driven drug discovery and molecular modelling.

Data Sources

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BioSimDB (Biomolecular Simulations Database)

Topology, trajectory, and AiiDA data provenance files from molecular dynamics simulations of biomolecules are stored in a repository specifically designed for their preservation and accessibility.

Tools

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Amber Plugin for AiiDA

The Amber plugin for AiiDA aims to enable the capture and sharing of the full provenance of data when parameterising and running molecular dynamics simulations.

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Demo BioSim Database With Local Web Interface

This demo application will create an SQLite database that can be used to include aiida archive files produced from several aiida plugins (aiida -gromacs and -amber presently). This database can be used to store and explore archive files and gives a taster for how biomolecular MD simulation data provenance can be stored for multiple research projects.

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GROMACS Plugin for AiiDA

The GROMACS plugin for AiiDA aims to enable the capture and sharing of the full provenance of data when parameterising and running molecular dynamics simulations.

Guidance

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Cloud Based Jupyter aiida-gromacs Demo/Training

Tutorials with pre-loaded user environments for using aiida-gromacs to produce provenance workflows for biomolecular simulations ( "Lysozyme MD simulation with aiida-gromacs" and "GPCR coarse-grained simulation setup with aiida-gromacs").