01. Workflow
1. Workflow
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Identify a target protein (discuss with supervisor).
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Find pdb files for your target (either from the RCSB PDB or from another source): make sure the experimental method (X-ray, NMR…) and the protein resolution are acceptable (normally less than 2.5Å); don’t forget to check the organism & expression system (e.g. E. Coli). You will need a pdb file of your target protein with a ligand bound.
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Examine the protein of interest in PyMOL: students will explore the different ways to view their protein’s structure and learn how to use PyMOL to view various pdb files with and without ligands bound. Students will be able to investigate binding interactions between the protein and bound ligands. Students will be able to come up with potential improvements and ideas for docking experiments.
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Use online databases to find compound datasets for docking experiments: searching online libraries such as PubChem, ChEMBL, Zinc15 and Enamine students can build compound datasets to use in molecular docking experiments.
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Design novel compounds in ChemDraw: students will design their own compounds in ChemDraw based on PyMOL analysis. These designs will be saved as sdf files and viewed in DataWarrior.
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Data processing in DataWarrior: students will examine the properties of the compounds found from the online databases and the designed compounds. Checking for key properties (LogP, MW, TPSA) and filtering out any undesirable compounds (such as those containing nasty functions, or particularly strained conformations).
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Energy minimisation of structures to be docked: 3D conformations of the structures to be used in docking experiments will be produced, these 3D conformations will be the minimised energy conformation of the compounds (required for docking). Lists of compounds to be docked will be saved as sdf files based on their 3D atom coordinates. sdf files for docking will be formed by manipulating text files to compile all designs/compounds for docking into a single sdf.
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Optimising the pdb files for docking - advanced processing techniques: to optimise the pdb files to be fit for docking experiments, extra computational tools are required. Protonation (opensource: H++/Propka), addition of missing loops or residues (opensource: Modeller) of a crystal structure (Dr Chris Swain can help with these using MOE)
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Molecular docking: students will design and perform their own molecular docking experiments by using a Jupyter notebook. Jobs will be performed on the UCL cluster via a VPN or on the students own machines if all required programmes are installed. (Command line techniques required.)
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Analysing the results: students will analyse the results from their docking experiments in DataWarrior and in PyMOL.
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Investigate the synthetic routes and feasibility of lead compounds: students can research the commercial availability and synthesis procedures involved in making their most promising compounds. Viable compounds could be suggested for synthesis at collaborating laboratories or made by the student themselves in the synthetic stage of their research projects.
