Computational chemistry with Galaxy
Welcome to the ChemicalToolbox — a webserver for processing, analysing and visualising chemical data, and performing molecular simulations. This server is a flavor of the European Galaxy instance, usegalaxy.eu.
Content
Get started
Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a guided tour through Galaxy’s user interface.
A good place to start is our tutorials, which provide an introduction to the cheminformatics and molecular dynamics tools in Galaxy.
You can also check out the standard but customizable workflows available there.
Almost a hundred different tools for cheminformatics and molecular dynamics have been integrated into the ChemicalToolbox. A selection are displayed below.
Get data
Compute chemical properties
Molecular docking
Pharmacophore alignment
Molecular dynamics simulation
| Tool | Description | Reference |
|---|
| gmxSetup | Produce a topology using GROMACS for a given protein structure | Abraham et al., 2015 |
| gmxSolvate | Solvate a system using GROMACS | Abraham et al., 2015 |
| gmxEM | Energy minimization using GROMACS | Abraham et al., 2015 |
| gmxSim | MD simulation using GROMACS | Abraham et al., 2015 |
| gmxRestraints | Calculate position restraints using GROMACS | Abraham et al., 2015 |
| gmxMakeNDX | Create an index file using GROMACS | Abraham et al., 2015 |
| gmxEnergy | Extract energy components using GROMACS | Abraham et al., 2015 |
| gmxTrj | Process MD trajectories using GROMACS | Abraham et al., 2015 |
| gmxEditconf | Structure configuration using GROMACS | Abraham et al., 2015 |
| gmxFEP | Alchemical free energy simulations using GROMACS | Abraham et al., 2015 |
| antechamber | Process input files with AmberTools | Case et al., 2005 |
| acpype | Produce GROMACS topologies with acpype | Sousa da Silva et al., 2012 |
Molecular dynamics analysis
| Tool | Description | Reference |
|---|
| mdaDistance | Distance analysis using MDAnalysis | Agrawal et al., 2011 |
| mdaDihedral | Dihedral analysis using MDAnalysis | Agrawal et al., 2011 |
| mdaRDF | Radial distribution function between two atoms | Agrawal et al., 2011 |
| mdaAngle | Angle analysis using MDAnalysis | Agrawal et al., 2011 |
| mdConverter | Interconvert between MD file formats | McGibbon et al., 2015 Abraham et al., 2015 |
| packmol | Create initial MD configurations | Martinez et al., 2009 |
| bio3dPCA | Apply PCA to an MD trajectory | Grant et al., 2006 |
| bio3dRMSD | Calculate RMSD for an MD trajectory | Grant et al., 2006 |
| bio3dRMSF | Calculate RMSF for an MD trajectory | Grant et al., 2006 |
Tutorials
🙋 Are additional tutorials needed? Please make a request.
Workflows
To orchestrate tools and help users with their analyses, several workflows are available. They formally orchestrate tools in a defined order and with defined parameters, but they are customizable (tools, order, parameters).
The workflows are available in the Shared Workflows, with the labels “cheminformatics” or “moleculardynamics”.
| Workflow | Description |
|---|
| Library preparation | Preparation of ligand library using PubChem, ChEMBL and ZINC |
| Protein-ligand docking | Docking with AutoDock Vina |
| Hole filling | Expanding a library into gaps in the chemical space |
| Cheminformatics-ML | Machine learning for predicting small molecule protein interactions |
| GROMACS | Molecular dynamics simulation with GROMACS |
| Bio3D | Molecular dynamics analysis with Bio3D |
| Zauberkugel | Pharmacophore-based target prediction of a bioactive ligand using Align-it |
Contributors
Citation
- Simon Bray, Xavier Lucas, Anup Kumar and Björn Grüning. “The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform”, Journal of Cheminformatics, doi: 10.1186/s13321-020-00442-7
- Tharindu Senapathi, Simon Bray, Christopher B Barnett, Björn Grüning, Kevin J Naidoo.
“Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)”, Bioinformatics, Volume 35, Issue 18, 15 September 2019, Pages 3508–3509, doi: 10.1093/bioinformatics/btz107
Our Data Policy
| Registered Users | Unregistered Users | FTP Data | GDPR Compliance |
|---|
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