00. Open Docking Lab Manual
Department of Chemistry
School of Pharmacy
Computational Molecular Docking Projects Using Open-Source Tools
A Guide to the Course
Version 1 (2020/21)
Contents
1. Workflow 2
2. Introduction 4
3. Getting pdb Files of your Target Protein 5
3.1 The Protein Data Bank 5
- Other Sources 5
4. PyMOL 6
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How to install PyMOL 6
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Viewing your Target Protein 7
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Looking at the Active Site 12
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Ligand Interactions 16
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Preparing Files for Molecular Docking Experiments 23
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How to Use the PyMOL Command Line 27
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Command Line Tutorial 27
5. Searching Online Databases 36
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PubChem 36
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ChEMBL 39
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Zinc15 43
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Enamine 45
6. DataWarrior 48
6.1 Installing DataWarrior 48
6.2 Viewing your Dataset in DataWarrior 50
6.3 Examining Properties and Useful Filters 52
6.4 Saving your Refined Dataset as a Single sdf File 57
6.5 Generating 3D Conformations of Compounds in 58 DataWarrior
7. Designing Compounds 61
7.1 ChemDraw3D Energy Minimisation of Compounds 61
8. Creating Single sdf files for docking 65
8.1 Manipulating Text Files 65
9. Molecular Docking Experiments 70
9.1 Accessing the UCL Cluster and Setting Up a VPN 70
9.2 Uploading your Files 71
9.3 How to Run the Jupyter Notebook 72
9.4 Google CoLab 81
10. Analysing Results 84
10.1 Analysing Results in DataWarrior 84
10.2 Viewing Poses in PyMOL 86
10.3 Checking Text Files – Ordering Results 89
10.4 2D Interaction Diagram 90
11. Additional Useful Resources 94
12. Glossary of Terms 95
13. Acknowledgements 96