| layout |
|---|
subsite-galaxy |
Welcome to our Computational Chemistry flavour of UseGalaxy.eu -- a webserver to process, analyse and visualize chemical data.
- 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.
Want to learn about computational chemistry? Check our tutorials.
Check also 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 |
|---|---|---|
| remSmallMol{:target="_top"} | Remove small molecules | N M O'Boyle,2011{:target="_blank"} |
| AddH{:target="_top"} | Add hydrogen atoms at a certain pH value | N M O'Boyle,2011{:target="_blank"} |
| RemDupMol{:target="_top"} | Remove duplicated molecules | N M O'Boyle,2011{:target="_blank"} |
| remProtState{:target="_top"} | Remove protonation state of every atom | N M O'Boyle,2011{:target="_blank"} |
| comConvert{:target="_top"} | Compound Convert Converts various chemistry and molecular modeling data files | N M O'Boyle,2011{:target="_blank"} |
| remConterIons{:target="_top"} | Remove counterions and fragments | N M O'Boyle,2011{:target="_blank"} |
| changTitle{:target="_top"} | Change Title to meta-data value | N M O'Boyle,2011{:target="_blank"} |
| remCountIo{:target="_top"} | Change Title to meta-data value | N M O'Boyle,2011{:target="_blank"} |
| {:.table.table-striped} |
| Tool | Description | Reference |
|---|---|---|
| genProp{:target="_top"} | Compute physico-chemical properties for a set of molecules | N M O'Boyle,2011{:target="_blank"} |
| NPL{:target="_top"} | Natural Product likeness calculator | Jayaseelan, Kalai Vanii, 2012{:target="_blank"} |
| QED | Drug-likeness quantitative estimation (QED) | Bickerton et al., 2012{:target="_blank"} |
| {:.table.table-striped} |
| Tool | Description | Reference |
|---|---|---|
| gmxSetup{:target="_top"} | Produce a topology using GROMACS for a given protein structure | Abraham et al., 2015{:target="_blank"} |
| gmxSolvate{:target="_top"} | Solvate a system using GROMACS | Abraham et al., 2015{:target="_blank"} |
| gmxEM{:target="_top"} | Energy minimization using GROMACS | Abraham et al., 2015{:target="_blank"} |
| gmxNVT{:target="_top"} | NVT equilibration using GROMACS | Abraham et al., 2015{:target="_blank"} |
| gmxNPT{:target="_top"} | NPT equilibration using GROMACS | Abraham et al., 2015{:target="_blank"} |
| gmxMD{:target="_top"} | Production simulation using GROMACS | Abraham et al., 2015{:target="_blank"} |
| mdaDistance{:target="_top"} | Distance analysis using MDAnalysis | Agrawal et al., 2011{:target="_blank"} |
| mdaDihedral{:target="_top"} | Dihedral analysis using MDAnalysis | Agrawal et al., 2011{:target="_blank"} |
| mdaRDF{:target="_top"} | Radial distribution function between two atoms | Agrawal et al., 2011{:target="_blank"} |
| mdaAngle{:target="_top"} | Angle analysis using MDAnalysis | Agrawal et al., 2011{:target="_blank"} |
| mdConverter{:target="_top"} | Interconvert between MD file formats | McGibbon et al., 2015{:target="_blank"} Abraham et al., 2015{:target="_blank"} |
| packmol{:target="_top"} | Create initial MD configurations | Martinez et al., 2009{:target="_blank"} |
| bio3dPCA{:target="_top"} | Apply PCA to an MD trajectory | Grant et al., 2006{:target="_blank"} |
| bio3dRMSD{:target="_top"} | Calculate RMSD for an MD trajectory | Grant et al., 2006{:target="_blank"} |
| bio3dRMSF{:target="_top"} | Calculate RMSF for an MD trajectory | Grant et al., 2006{:target="_blank"} |
| {:.table.table-striped} |
- PDF's of the workshop run in 2019 are available
🙋 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} |
{% bibliography --cited --prefix index-metagenomics --group_by none %}