Advanced Structure-Based Drug Design
Pharmacophore Modeling / Docking / Fragment-Based Design / Scaffold Replacement / R-Group Screening / Project Search / Protein-Ligand Interaction Fingerprints (PLIF)
This workshop explores advanced structure-based drug design (SBDD) workflows used in drug discovery projects. Participants will learn about key topics, including pharmacophore query generation, protein-ligand docking, scaffold replacement, and R-group screening. The session will cover the application of pharmacophore searching in drug design, as well as methods for querying 3D project databases. Additionally, participants will generate and analyze protein-ligand interaction fingerprints (PLIF) to support their design strategies.

 Peptide Modeling, Conformational Searching and Docking
Structure preparation / Non-natural amino acids / Protein Design / Conformational searching / Distance restraints / Peptide-Protein docking / Protein-Ligand Interaction Fingerprints (PLIFs)
This workshop focuses on methods for analyzing and optimizing peptide-protein interactions in the binding site. Participants will learn peptide-protein structure preparation, peptide sequence optimization using both natural and non-natural amino acids, and perform conformational analysis. Peptide-protein docking will be demonstrated, along with tools for analyzing protein-ligand interactions to assess contact points. Advanced conformational searching techniques using distance restraints will also be described.