How does Glide use confgen during a docking simulation?

A population of ligand conformers is generated first with confgen, independent of the receptor/grid. Each conformer is then docked into the binding pocket via molecular, rotational, and translation motions.

Please note that confgen in Glide is not exactly the same thing as the ConfGen product in Maestro. Glide does not run the ConfGen product, but it does run routines and libraries that are similar to or shared with ConfGen. Both confgen in Glide and ConfGen use the same basic search methodology, which is described in Chapter 2 of the Glide User Manual, or Chapter 1 of the ConfGen User Manual. There are some differences in the default parameters used by Glide (e.g., a ring conformation energy window of 2.5 kcal/mol rather than ~12 kcal/mol). Also, Glide divides the ligand into core and peripheral rotatable bonds, generates core conformations, and then docks the core plus peripheral group rotamers as a single object, rather than immediately producing conformations of the full molecule with particular peripheral group rotamers. Glide does not rank conformers, but keeps all of them, subject to its limits on the number of core conformers and application of constraints.

Keywords: ConfGen, confgen, conformers, generate, dock, Glide

Related Articles:

#641: Does Glide docking include a global conformation search?

Back to Search Results