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The paper presented an advance in docking technology that has been at the heart of Schrödinger’s software suite since. Standard Precision Glide (SP) is introduced in detail and includes terms for hydrophobic interactions, hydrogen bonds of charged and neutral types, metal interactions, a rotational bond penalty (for conformational entropy), coulombic and van der Waals terms.  In addition a solvation term considers water molecule presence. This glidescore is used to predict binding free energy and a combination of glidescore with molecular mechanics interaction energy and ligand strain energy to select docked poses. It is curious that it was necessary to scale the van der Waals’ radii (effectively shrink the atoms) to fit some known actives into their cognate binding sites. The effectiveness of the approach for correctly positioning ligands in the crystal structure they came from was compared to that with GOLD and FlexX. The test set used included those used for these other approaches and involved 282 complexes taken from crystal structures. To avoid bias from the ligand geometry, these were all created from scratch from 2D structures.

“Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy”  by Friesner, Banks, Murphy, Halgren, Klicic, Mainz, Repasky, Knoll, Shelley, Perry, Shaw, Francis and Shenken.

DOI: 10.1021/jm0306430

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