The document describes a study that identified benzene clusters in a protein in order to create a pharmacophore model. Researchers used PyMol to save the molecule containing benzenes and then used LigandScout to generate a pharmacophore model based on the specific benzenes identified (benzenes 1, 13, 21, and 26). The pharmacophore model was created to represent the hot spots in the protein-ligand interaction.

1. Benzene Identification of a Protein
to Produce a Pharmacophore Model
RISE Program
Alberto Cintron
Nicole Colon
Natalia Manzano
Wilmarie Morales
Mentor: Carlos Santos

2. Objectives
• Benzene Clusters Identification
• Creating a Pharmacophore Model using the hot spots
identified by the clusters identification

3. Terminology
• Hot spots:
• Pharmacophore Model
• Benzenes
• Cluster

4. Methodology
• Part I
• Using the PyMol Program we saved the molecule with the
benzenes.
• Part II
• Using LigandScout we produce the pharmacophore model
• Generate the model using the specific benzenes(1, 13, 21, 26)

5. Benzene 1

6. Benzene 2

7. Benzene 3

8. Benzene 4

9. Pharmacophore Model