CSD-Discovery Workshops
These self-guided workshops are tutorials intended to demonstrate the various tools and features of the CSD-Discovery suite including GOLD, CSD- CrossMiner, Hermes.
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Introduction to Full Interaction Maps
This is a self-guided workshop on how to use the full interaction maps for exploring crystal structures; including assessing hydrogen bonding and substituent effects.
Prerequisites: This handout is also part of the CSDU module Analysing intermolecular interactions 101 – Full Interaction Maps. Visit the module webpage to learn more about FIMs, and for more demos and tips.
Workshop code: MER-002
Understand Protein-Ligand Interaction Patterns Using Full Interaction Maps (FIMs)
This is a self-guided workshop on how to generate full interaction maps of protein-ligand interaction patterns and analyse docking solutions with FIMs.
Prerequisites: Introduction to Hermes (HERM-001)
Workshop code: MER-004
How to Generate Ensembles of Conformers using the CSD Conformer Generator
This is a self-guided workshop on how to generate ensembles of conformers using the command line function, Mercury and the CSD Python API
Prerequisites: Basic knowledge of Mercury, if you are new to Mercury, you can start with the Visualisation workshop – MER-001, try the CSDU module Visualization 101 – Visualizing structural chemistry data with Mercury. A basic understanding of Python and the command line, Introduction to the CSD Python API – PYAPI-001.
Workshop code: CONF-002
Introduction to Protein-Ligand Docking with GOLD
This is a self-guided workshop on the basics of protein-ligand docking in GOLD, demonstrating how to set up, run and analyse your docking results.
Prerequisites: Introduction to Hermes – HERM-001
Workshop code: GLD-001
Ensemble Docking with GOLD
This is a self-guided workshop on the how to perform non-native docking of a ligand into an ensemble of conformers, accounting for movements of the protein backbone.
Prerequisites: Introduction to Hermes – HERM-001, Introduction to Protein-Ligand docking in GOLD – GLD-001
Workshop code: GLD-002
Pose Prediction with GOLD
This is a self-guided workshop on the how to perform pose prediction with GOLD, focusing on building a correct representation of the protein binding site and choosing high accuracy settings.
Prerequisites: Introduction to Hermes – HERM-001, Introduction to Protein-Ligand docking in GOLD – GLD-001
Workshop code: GLD-003
Pharmacophore Constraints in GOLD
This is a self-guided workshop on the how to include pharmacophore constraints during protein-ligand docking in GOLD.
Prerequisites: Introduction to Hermes – HERM-001, Introduction to Protein-Ligand docking in GOLD – GLD-001
Workshop code: GLD-004
Flexibility and Constraints in GOLD
This is a self-guided workshop on the how to inspect a protein crystal structure to determine how to include flexible sidechains in your sampling.
Prerequisites: Introduction to Hermes – HERM-001, Introduction to Protein-Ligand docking in GOLD – GLD-001
Workshop code: GLD-005
Docking with Waters in GOLD
This is a self-guided workshop on the how to perform docking into a binding site that contains water molecules.
Prerequisites: Introduction to Hermes – HERM-001, Introduction to Protein-Ligand docking in GOLD – GLD-001
Workshop code: GLD-006
