This protocol is designed to help in analysis of protein family profile. It aligns each protein to a reference protein for binding site analysis, extract aligned bound ligands, and then generate a fragment library for further De Novo Design or Fragment-based Design.

What are the processes in this protocol?
[1]specify the folder that contains multiple PDB files, specify the reference protein w/ its ligand that needs to be loaded into DS and be used to define all the binding site residues (by radius).
[2]align each protein against reference based on 3D similarity, then make a tight superimposition using bindingsite residues, finally save out individual aligned protein in pdb (protein_aligned.pdb). All bindingsite residue information will be saved as well (including rmsd).
[3]extract out all the aligned ligands then save them as sd file (overlay_ligand.sd).
[4]fragmentize each aligned ligand, filter out desired one and then save them all as a fragment library (fragment.sd). The fragment will maintain its 3D coordinate.

*Requirement: PP Chemistry component collection in addition to DS.

This protocol can be run through either PP or DS (DS is recommended as the job is easy to set up). Attached pls find the updated protocol with an example...

(Thanks to Marc Fasnacht and Sumeet Salaniwal, as this protocol was built on top of their published protocols)