Notes on using eSimDock webserver

eSimDock webserver accepts two submission types:

New submission. You will need the following input files to use this option:

The quality of anchor ligands is very important to obtain reliable binding affinity estimates. Using this option, you have a full control on the selection of molecules that are subsequently used as anchor ligands in similarity-based docking. This is also useful for e.g. processing a series of derivatives that share a common scaffold; you can use the scaffold molecule as a single anchor for docking compounds with different R groups.

Use eFindSite pocket. This is a more convenient option, which requires running eFindSite webserver first. Here, you will need only the query compounds in SDF format (e.g. HSPCA-BindingDB.sdf) and a 10-digit ticket generated by eFindSite. You will also need to specify which predicted pocket is the target site for ligand docking. eSimDock will use the target structure submitted to eFindSite webserver; anchor ligands will be generated automatically from evolutionarily related proteins identified by eThread. Using this option, you may expect satisfactorily results in terms of binding pose prediction accuracy (depending on the similarity of your query compounds to the identified anchor ligands); however, binding affinity prediction may be less accurate.

 

© Michal Brylinski
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