I'm looking for server or free software to create a pharmacophore based on the 3D structure of my protein only not based on the complex of protein and ligand
Two free softwares: fpocket (fpocket.sourceforge.net/) and Ligbuilder-2 (www.ligbuilder.org/intro.html) generate structure-based pharmacophare by using 3D-structure of the protein only. But these two softwares run on Linux operating system.
Hii,, In terms of server you can use ZincPharmer. You can upload your protein and define the pharmacophores as per your choice. After that you can also perform a query search which will bring out a variety of ligands which can further used for virtual screening. Enable JAVA plugin of your browser. Hope you will have a good experience.