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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