Structure-Based Design Active Site Detection & Visualization Protein: Ligand Interaction Diagrams Contact Statistics, Electrostatic, & Interaction Maps Scaffold Replacement, Fragment Linking/Growing Ligand-Receptor Docking Multi-Fragment Search BREED: 3D Ligand Generator Medicinal Chemistry Transformation Pharmacophore Discovery Ligand & Structure-Based Query Editor Partial Matches, SMARTS Patterns, Constraints, Shape Custom Features, Boolean Expressions Automatic Query Generation High-Throughput Conformation Generation Pharmacophore Search (.mdb, .oeb) Linker & Lead-like Conformational Databases Ligand & Structure-Based Scaffold Replacement Protein & Antibody Modeling Protonate3D: Protonation State Prediction Protein Structure, Family, & Fab Databases Remote Homology & Fold Identification Multiple Sequence/Structure Alignment & Analysis Homology Modeling & Macromolecular Simulation Knowledge-based Antibody Modeling Mutation & Rotamer Exploration Protein Geometry Quality Assessment Molecular Modeling & Simulations MMFF, Amber, CHARMM Forcefields Explicit or Implicit Solvent Models Molecular Mechanics & Dynamics Conformation Generation, Analysis, and Clustering Molecular Surfaces & Electron Density Display Non-linear Poisson-Boltzmann Electrostatics Quantum and Semi-Empirical Calculations Cheminformatics & (HTS) QSAR SD Command Tools for Pipeline Workflows Washing, Filtering, Tautomer & Titration Enumeration 600+ Molecule Descriptors PLS, PCR, Binary QSAR, & Recursive Partitioning Similarity, Diversity, & Fingerprints 3D Conformer Generation from SMILES or 2D Combinatorial Library Design Automatic Publication-Quality 2D Depiction Medicinal Chemistry Applications MOE/web: Web Browser Applications Protein: Ligand Interaction Diagrams Contact Statistics, Electrostatic, & Interaction Maps LigX: Ligand Optimization in Pocket Ligand & Structure-Based Scaffold Replacement Multiple Molecule Flexible Alignment Conformation Generation, Analysis, & Clustering Synthetic Feasibility Descriptor Methods Development & Deployment Scientific Vector Language (SVL) Background (batch) & Cluster Computing Platform Independent (Windows, Mac OS X (10.5 and 10.6), Linux, Unix) URL (HTTP/FTP) & TCP-IP Sockets Relational Database Connectivity (JDBC) MOE/web: Web Browser Application Framework Soap Server, KNIME nodes   Request Information System Requirements