BioSim (Biomolecular Simulations) Data Resources

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.

Landing Page

PSDI Community Data Collection - BioSimDB

You can see the resources that are part of this resource theme below.

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Showing 4 of 4 resources

Data Sources

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

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.

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

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").

Creators

James Gebbie-Rayet & Jas Kalayan

Keywords and Subjects

PSDI-pathfinder

molecular dynamics

biomolecular simulation

trajectory

gromacs

amber

namd

lammps

protein dynamics

drug discovery

pdb

biomolecules

proteins

dna

membranes

provenance

enhanced sampling

metadynamics

free energy

alchemical free energy

protein folding

alphafold

machine learning

database

data storage

structural biology

computational biology

computational biochemistry

computational chemistry

simulation software

molecular biology

soft matter physics

What We Provide