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 for drug discovery projects, covering a broad range of topics from pharmacophore query generation to protein-ligand interaction fingerprints (PLIF). Participants will learn about the application of pharmacophores in protein-ligand docking, scaffold replacement, and R-group screening. Additionally, the workshop will present a method for querying a 3D project database, as well as techniques for generating and analyzing protein-ligand interaction fingerprints (PLIF).

Protein-Ligand Interaction Analysis / Pharmacophore Modeling / Docking / Protein-Ligand Interaction Fingerprints (PLIF) / Fragment-based Design / Scaffold Replacement

Protein Alignments and Superposition / Loop and Linker Modeling / Homology Modeling / Protein-Protein Docking / Epitope Analysis / Protein Properties / Protein Solubility Prediction / Protein Patches (2D and 3D) / Biologics QSAR/QSPR Modeling

Protein-Protein Interaction Analysis / Molecular Surfaces / Protein Patch Analysis / Protein Properties / Protein Engineering / Antibody Homology Modeling / Antibody Database / Developability Analysis

Peptide Complex Preparation / Protein-Peptide Interaction Analysis / Surfaces and Maps / Peptide Sequence Optimization / Non-Natural Amino Acids / Conformational Searching / Peptide-Protein Docking / Protein-Peptide Interaction Fingerprints

Protein-Ligand Interaction Analysis / Protein-Ligand Docking / Pharmacophore Modeling / High-throughput Docking / Template-Based Docking / Covalent Docking

This workshop will cover protein-ligand docking to predict the binding of small-molecule structures to a protein target. Pharmacophore-guided docking will be described as a method to preserve key interactions. Template-based docking will be used to efficiently dock congeneric series of compounds. Reaction-based covalent docking will be used to generate poses for covalently bound ligands. In addition, analysis of docking results and techniques to achieve high-throughput docking will be addressed.

Scaffold Replacement / Ligand Growing / R-group Screening / Bioisosteric Transformations / Pharmacophore Modeling

This workshop will cover fragment-based drug design applications, focusing on methods such as scaffold hopping, fragment growing and R-group exploration to generate novel compound ideas, optimizing and scoring the structures in the pocket. The use of molecular descriptors and pharmacophore models to guide the drug design processes will also be discussed. In addition, an SBDD method for generating closely related analogs through bioisosteric replacements will be presented.