Register training material
8 materials found

Keywords: R-programming  or computational-chemistry 


Hands-on for 'Protein-ligand docking' tutorial

The questions this addresses are:
- What is cheminformatics?
- What is protein-ligand docking?
- How can I perform a simple docking workflow in Galaxy?

The objectives are:
- Create a small compound library using the ChEMBL database
- Dock a variety of ligands to the active site of the...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Protein target prediction of a bioactive ligand with Align-it and ePharmaLib' tutorial

The questions this addresses are:
- What is a pharmacophore model?
- How can I perform protein target prediction with a multi-step workflow or the one-step Zauberkugel workflow?

The objectives are:
- Create an SMILES file of a bioactive ligand.
- Screen the query ligand against a...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring' tutorial

The questions this addresses are:
- How can candidate ligands be generated and docked to a protein in Galaxy?
- How can the poses of the docked ligands be evaluated?
- How can a workflow for drug virtual screening be constructed in Galaxy?

The objectives are:
- Understand how Galaxy was...

Keywords: computational-chemistry, covid19

Resource type: hands-on tutorial

Hands-on for 'Running molecular dynamics simulations using GROMACS' tutorial

The questions this addresses are:
- How do I use the GROMACS engine in Galaxy?
- What is the correct procedure for performing a simple molecular dynamics simulation of a protein?

The objectives are:
- Learn about the GROMACS engine provided via Galaxy.
- Understand the structure of the...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Analysis of molecular dynamics simulations' tutorial

The questions this addresses are:
- Which analysis tools are available?

The objectives are:
- Learn which analysis tools are available.
- Analyse a protein and discuss the meaning behind each analysis.

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'High Throughput Molecular Dynamics and Analysis' tutorial

The questions this addresses are:
- How are protein-ligand systems parameterized for molecular dynamics simulation?
- What kind of analysis can be carried out on molecular trajectories?
- How can high-throughput MD be used to study multiple ligands?

The objectives are:
- Learn about...

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Running molecular dynamics simulations using NAMD' tutorial

The questions this addresses are:
- How do I use the NAMD engine in Galaxy?
- What is the correct procedure for performing a simple molecular dynamics simulation of a protein?

The objectives are:
- Learn about the NAMD engine provided in BRIDGE

Keywords: computational-chemistry

Resource type: hands-on tutorial

Hands-on for 'Setting up molecular systems' tutorial

The questions this addresses are:
- How to get started modelling a protein and a ligand?

The objectives are:
- learn about the Protein Data Bank
- learn how to set up up a model protein and ligand system (with CHARMM-GUI)
- learn how to upload the system to Galaxy

Keywords: computational-chemistry

Resource type: hands-on tutorial