Generate diverse lead compounds for a specific protein target using structure-based drug design with MolCraft. Use this skill when: (1) Designing drug candidates for a known protein target (PDB ID or disease name), (2) Generating structurally diverse molecules with optimized binding affinity, (3) Filtering candidates…
Use at the start of any computational chemistry task to structure thinking, map available tools, and generate concrete hypotheses. Covers molecule evaluation, hypothesis building, reaction assessment, and pipeline design. Flexible guide — adapt depth to problem complexity.
Use when performing protein-ligand docking, virtual screening, or structure-based drug design. Covers receptor preparation (protonation, pocket definition), AutoDock Vina/Gnina docking engines, high-throughput virtual screening pipelines, pose analysis with interaction fingerprints, and ensemble docking for protein…
Use when working with PepFlex for in silico peptide screening and evolutionary optimization. Handles peptide population management, mutation, crossover, custom evaluation pipelines, and multi-round evolutionary simulation.