Here are the slides for the talk I gave last Friday on Protein-Ligand Docking at the EBI Small-Molecule Bioactivites course.
For three or so slides I drew heavily from Leach and Gillet's "Introduction to Cheminformatics", which I recommended to the course participants.
To follow the slides, I prepared a self-guided tutorial that used the GOLD docking software to dock ligands taken from Kinase SARfari to a kinase crystal structure taken from the PDB. If this is of interest, let me know.
Note to self: (1) Add something on evaluation of pose prediction using cross docking. (2) ROC curve. (3) Do worked example of enrichment calculation.
ReplyDeleteNote to self: (4) Do an example docking (5) Skim through a paper that does a docking (6) More interactivity - who has used docking before? has it worked, etc.? problems encountered. could this be useful for you in future? (7) Show how to use ZINC, etc. to select appropriate inactives for calculating enrichment.
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