MOE Project for Organizing SBDD Data • Create SBDD project databases with automated protocols • Align and prepare protein structural databases containing surfaces, maps & descriptors • Enrich homology modeling and loop searching with specialized protein family databases Focused Protein and Antibody Libraries - Virtual Phage Display • Calculate frequency and probability of amino acids at residue mutation sites • Reduce the mutation space with mutation probability scoring • Enrich the number of actives through stability and affinity scoring Quantum Mechanical Refinement of Conformations and Energy Minimization • Rapidly generate MM conformations and refine with QM • Apply a new robust multi-stage automatic QM refinement protocol for Gaussian • Calculate accurate geometries and energetics through MOE/web SOAP functions for QM Template Forced Docking and Molecular Superposition • Select a ligand substructure for template-based docking • Dock using similarity for maximum substructure matching • Align and superpose a database of molecules for ligand based drug design projects Non-natural Amino Acid Support for Protein and Peptide Design • Use the integrated protein builder to model natural and synthetic protein hybrids • Build non-natural amino acid (NNAA) sequences in real-time and explore conformations • Model and virtually optimize NNAA linkers for antibody-drug conjugates (ADC) Specialized Protein Family Databases and Search Interface • Augment specialized protein family databases (GPCR, Kinase, etc.) with in-house data • Query protein family databases by structure, sequence and ligand similarity • Analyze protein-ligand interaction fingerprints on large sets of protein complexes