Peptide Modeling in MolSoft ICM-Pro Interactive Ligand Editor

Learn advanced peptide modeling techniques using MolSoft ICM-Pro's Interactive Ligand Editor in this comprehensive 12-minute tutorial. Master the preparation, editing, and optimization of peptides through specialized sequence-level tools and continuous chain handling methods. Begin by understanding how to merge peptides into single molecules and convert them to ICM format, then enable peptide mode in the Ligand Editor to ensure proper continuous chain handling and correct backbone geometry. Explore step-by-step residue operations including inserting, deleting, replacing residues, and adding Acetyl/NH₂ caps to peptide structures. Discover refinement and minimization techniques using the "Relax" function to fix covalent geometry, "Reinforce Helix" to tighten helical regions, and methods for optimizing sidechains and minimizing torsions. Gain expertise in peptide stapling by utilizing the staple library with hydrocarbon and specialty chemistries to create covalent links at I+4 or I+7 positions. Learn to monitor RTCNN scores and LigStrain metrics to evaluate model quality throughout the modeling process. Practice these techniques using the example PDB 7UWI featuring Beta-Catenin in complex with a Helicon Peptide, providing hands-on experience with real molecular structures in computational drug design and peptide therapeutics development.