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Computational chemistry with Galaxy


Cheminformatics

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.

  1. TOC {:toc}

Get started

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 cheminformatics and molecular dynamics tools in Galaxy.

You can also check out the standard but customizable workflows available there.

Tools

Almost a hundred different tools for cheminformatics and molecular dynamics have been integrated into the ChemicalToolbox. A selection are displayed below.

Get data

Tool Description Reference
{% include tool.html id="pubchem" %} Download all compounds from PubChem Kim et al., 2016{:target="_blank"}
{% include tool.html id="chembl" %} Download molecules from ChEMBL Davies et al, 2015{:target="_blank"}
{% include tool.html id="pdb" %} Download a file from the Protein Data Bank Berman, 2000{:target="_blank"}
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Chemical structure conversion and manipulation tools

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"}
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Compute chemical properties

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"}
{% include tool.html id="mordred" %} Molecular descriptor calculator Moriwaki et al., 2018{:target="_blank"}
{% include tool.html id="chemfp" %} Fingerprints with chemfp Dalke, 2013{:target="_blank"}
{% include tool.html id="tbClust" %} Taylor-Butina clustering Dalke, 2013{:target="_blank"}
{% include tool.html id="nxnClust" %} NXN clustering Dalke, 2013{:target="_blank"}
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Molecular docking

Tool Description Reference
{% include tool.html id="vina" %} Docking with AutoDock Vina Trott et al., 2009{:target="_blank"}
{% include tool.html id="rbdock" %} Docking with rDock Ruiz-Carmona et al., 2014{:target="_blank"}
{% include tool.html id="sucos" %} Score docked poses using SuCOS Leung et al., 2019{:target="_blank"}
{% include tool.html id="fpocket" %} Search a protein for potential binding sites Schmitdke et al., 2010{:target="_blank"}
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Pharmacophore alignment

Tool Description Reference
{% include tool.html id="alignit" %} Feature alignment using Align-it Taminau et al., 2008{:target="_blank"}
{% include tool.html id="sucos_clustering" %} Feature clustering using SuCOS Leung et al., 2019{:target="_blank"}
{% include tool.html id="Open3DALIGN" %} Unsupervised molecular alignment using RDKit Tosco et al., 2011{:target="_blank"}
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Molecular dynamics simulation

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="gmxSim" %} MD simulation using GROMACS Abraham et al., 2015{:target="_blank"}
{% include tool.html id="gmxRestraints" %} Calculate position restraints using GROMACS Abraham et al., 2015{:target="_blank"}
{% include tool.html id="gmxMakeNDX" %} Create an index file using GROMACS Abraham et al., 2015{:target="_blank"}
{% include tool.html id="gmxEnergy" %} Extract energy components using GROMACS Abraham et al., 2015{:target="_blank"}
{% include tool.html id="gmxTrj" %} Process MD trajectories using GROMACS Abraham et al., 2015{:target="_blank"}
{% include tool.html id="gmxEditconf" %} Structure configuration using GROMACS Abraham et al., 2015{:target="_blank"}
{% include tool.html id="gmxFEP" %} Alchemical free energy simulations using GROMACS Abraham et al., 2015{:target="_blank"}
{% include tool.html id="antechamber" %} Process input files with AmberTools Case et al., 2005{:target="_blank"}
{% include tool.html id="acpype" %} Produce GROMACS topologies with acpype Sousa da Silva et al., 2012{:target="_blank"}
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Molecular dynamics analysis

Tool Description Reference
{% 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"}
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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
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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
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