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.

This workshop explores structure-based methods for oligonucleotide design and optimization, covering siRNA design, nucleotide modifications and aptamer engineering. Participants will use sequence data to construct siRNA duplexes with different modification patterns. Molecular surfaces will be generated to assess properties such as electrostatics and steric complementarity, helping identify opportunities for nucleotide optimization and evaluate the effects of chemical modifications on affinity and stability. These structure-based approaches will also be applied to aptamer engineering through analysis of the thrombin-bound RNA aptamer interface, focusing on steric fit and key interactions. Finally, RNA-protein docking will be explored, including the analysis of predicted binding poses and key molecular interactions.