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Can I dock peptides as ligands in Glide?

As of the 2013-2 release, Glide has a special peptide docking mode that is designed to handle the much greater flexibility of peptides relative to the usual kinds of ligands. This mode has enhanced sampling and other settings that enable it to capture a wider range of poses. To use this mode, choose SP Peptide from the Precision option menu in the Settings tab of the Ligand Docking panel. For more information, see the help topic or the Glide User Manual.

The 2013-3 Biologics Suite (BioLuminate) introduced a Peptide Docking panel, in which small peptides of 16 residues or less can be provided by sequence, docked with Glide, and scored with MM-GBSA, as described in a recent publication. The Biologics Suite also offers access to Piper, a program for protein-protein docking, which can be used for large peptides (note that this program performs completely rigid docking).

Glide has a limit on the size of the ligand: as of the 2015-1 release, it can handle ligands with up to 500 atoms and 100 rotatable bonds (300 and 50 in previous releases). These limits should be adequate for many peptides. If any your peptide ligands are within the atom limit but have more rotatable bonds, you can decrease the number of rotatable bonds sampled by freezing amide bonds at their input conformations (on the Settings tab of the Ligand Docking panel). This might help you get under the rotatable bond limit. You can also decrease the number of rotatable bonds by applying torsional constraints (on the Torsional Constraints tab of the Ligand Docking panel). For example, to freeze the peptide backbone, use the SMARTS pattern "C(=O)-NH-C-C(=O)-NH" and constrain all torsions in the pattern.

An alternative approach for peptides with too many rotatable bonds for flexible docking is to generate the conformers outside Glide (e.g. with MacroModel), and then dock them rigidly, as rigid docking does not have the rotatable bond limit.

Keywords: peptide-protein docking, LLMOD method

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