| layout | subdomain |
|---|---|
subsite-galaxy |
cheminformatics |
Welcome to our Computational Chemistry flavour of UseGalaxy.eu -- a webserver for processing, analysing and visualising chemical data, and performing molecular simulations.
- TOC {:toc}
Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take a guided tour{:target="_blank"} through Galaxy's user interface.
A good place to start is our tutorials, which provide an introduction to the molecular dynamics tools in Galaxy.
You can also check out the standard but customizable workflows available there.
Several tools are integrated in this custom Galaxy instance. They were chosen for their use in exploitation of chemical data:
| Tool | Description | Reference |
|---|---|---|
| {% include tool.html id="remSmallMol" %} | Remove small molecules | N M O'Boyle,2011{:target="_blank"} |
| {% include tool.html id="AddH" %} | Add hydrogen atoms at a certain pH value | N M O'Boyle,2011{:target="_blank"} |
| {% include tool.html id="RemDupMol" %} | Remove duplicated molecules | N M O'Boyle,2011{:target="_blank"} |
| {% include tool.html id="remProtState" %} | Remove protonation state of every atom | N M O'Boyle,2011{:target="_blank"} |
| {% include tool.html id="comConvert" %} | Compound Convert Converts various chemistry and molecular modeling data files | N M O'Boyle,2011{:target="_blank"} |
| {% include tool.html id="remConterIons" %} | Remove counterions and fragments | N M O'Boyle,2011{:target="_blank"} |
| {% include tool.html id="changTitle" %} | Change Title to meta-data value | N M O'Boyle,2011{:target="_blank"} |
| {% include tool.html id="remCountIo" %} | Change Title to meta-data value | N M O'Boyle,2011{:target="_blank"} |
| {:.table.table-striped} |
| Tool | Description | Reference |
|---|---|---|
| {% include tool.html id="genProp" %} | Compute physico-chemical properties for a set of molecules | N M O'Boyle,2011{:target="_blank"} |
| {% include tool.html id="NPL" %} | Natural Product likeness calculator | Jayaseelan, Kalai Vanii, 2012{:target="_blank"} |
| {% include tool.html id="QED" %} | Drug-likeness quantitative estimation (QED) | Bickerton et al., 2012{:target="_blank"} |
| {:.table.table-striped} |
| Tool | Description | Reference |
|---|---|---|
| {% include tool.html id="gmxSetup" %} | Produce a topology using GROMACS for a given protein structure | Abraham et al., 2015{:target="_blank"} |
| {% include tool.html id="gmxSolvate" %} | Solvate a system using GROMACS | Abraham et al., 2015{:target="_blank"} |
| {% include tool.html id="gmxEM" %} | Energy minimization using GROMACS | Abraham et al., 2015{:target="_blank"} |
| {% include tool.html id="gmxNVT" %} | NVT equilibration using GROMACS | Abraham et al., 2015{:target="_blank"} |
| {% include tool.html id="gmxNPT" %} | NPT equilibration using GROMACS | Abraham et al., 2015{:target="_blank"} |
| {% include tool.html id="gmxMD" %} | Production simulation using GROMACS | Abraham et al., 2015{:target="_blank"} |
| {% include tool.html id="mdaDistance" %} | Distance analysis using MDAnalysis | Agrawal et al., 2011{:target="_blank"} |
| {% include tool.html id="mdaDihedral" %} | Dihedral analysis using MDAnalysis | Agrawal et al., 2011{:target="_blank"} |
| {% include tool.html id="mdaRDF" %} | Radial distribution function between two atoms | Agrawal et al., 2011{:target="_blank"} |
| {% include tool.html id="mdaAngle" %} | Angle analysis using MDAnalysis | Agrawal et al., 2011{:target="_blank"} |
| {% include tool.html id="mdConverter" %} | Interconvert between MD file formats | McGibbon et al., 2015{:target="_blank"} Abraham et al., 2015{:target="_blank"} |
| {% include tool.html id="packmol" %} | Create initial MD configurations | Martinez et al., 2009{:target="_blank"} |
| {% include tool.html id="bio3dPCA" %} | Apply PCA to an MD trajectory | Grant et al., 2006{:target="_blank"} |
| {% include tool.html id="bio3dRMSD" %} | Calculate RMSD for an MD trajectory | Grant et al., 2006{:target="_blank"} |
| {% include tool.html id="bio3dRMSF" %} | Calculate RMSF for an MD trajectory | Grant et al., 2006{:target="_blank"} |
| {:.table.table-striped} |
- Visit the Galaxy training website for tutorials on using the Galaxy tools for molecular dynamics.
🙋 Are additional tutorials needed? Please make a request.
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 label "cheminformatics".
| Workflow | Description |
|---|---|
| GROMACS | Molecular dynamics simulation with GROMACS |
| Bio3D | Molecular dynamics analysis with Bio3D |
| {:.table.table-striped} |
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