Macrocyclic lead optimisation
Macrocycles are becoming increasingly popular in drug discovery, due to their vast potential against previously “undruggable” targets. But the size…
SeeSAR Pose in StarDrop cannot dock covalent molecules. However, these can be treated like other non-covalent ligands where the bond to the receptor is absent.
The templated docking where you can edit a docked molecule could be particularly helpful here. If the part of the molecule that forms the covalent bond is correctly placed in the binding site (without the covalent bond) then the rest of the molecule can be edited and poses explored there while keeping the key covalent binding region similar to that of the template.
The Reference Guide Section 13.5 describes the docking algorithm used (FlexX). The guide can be accessed the Help menu in StarDrop.
More structured-based design resources
3D virtual screening with Surflex eSim3D
When exploring chemistry space around a known hit or lead, you can use 3D virtual screening to identify new compounds…
Extrapolative prediction using physically-based QSAR
Surflex-QMOD integrates chemical structure and activity data to produce physically-realistic models for binding affinity prediction.
