3D Molecular Visualization

  • Easy-to-Use Graphical Interface
  • Active Site Detection and Analysis
  • Molecular Surfaces and Electron Density
  • Visualize Non-bonded Interactions
  • Publication-Quality Images and Movies
  • GPU Accelerated 3D Stereo Graphics
  • Mixed Virtual Reality and 3D Printing

Structure-Based Design

  • Streamlined Interface for Ligand Design
  • Active Site Detection and Analysis
  • Interactive Ligand Design in the Pocket
  • Protein-Ligand Interaction Diagrams
  • Predict Water Sites and Energetics
  • Induced-Fit Docking
  • Link, Grow and Replace Fragments

Antibody and Biologics Design

  • Structure-Based Protein Engineering
  • Assess Liabilities and Developability
  • Optimize Affinity, Stability and Solubility
  • High-Throughput Antibody Modeling
  • Generate Virtual Libraries
  • Protein Docking and Epitope Mapping
  • Model ADCs and Fusion Proteins

MOEsaic - SAR Explorer

  • SAR and SPR Visualization
  • Free-Wilson Compound Suggestions
  • Matched Molecular Pairs
  • R-Group Analysis and Profiling
  • Substructure and Similarity Search
  • Design Novel Virtual Compounds
  • Document Ideas and Share Sessions

Ligand-Based Design

  • Conformation Generation and Clustering
  • Align and Superpose Small Molecules
  • MOEsaic for SAR Exploration
  • Pharmacophore Elucidation and Screening
  • Generate QSAR Models – MOE Descriptors
  • Torsion Profiles for Conformation Analysis
  • Combinatorial Library Enumeration

Protein, DNA/RNA Modeling

  • Visualize Proteins, Patches, and Interfaces
  • Predict 3D Protein Structure from Sequence
  • Build DNA/RNA Models
  • Explore Mutations and Rotamers
  • Molecular Dynamics Simulations
  • Loop/Linker Searching and Sampling
  • Protein-Protein Docking

Virtual Screening

  • 3D Pharmacophore Screening
  • Shape and Feature Constraints
  • Small Molecule Docking
  • 2D and 3D Fingerprint Screening
  • Scaffold and Fragment Replacement
  • Conformation Databases
  • Reaction-Based Library Design

Fragment-Based Discovery

  • Scaffold Hopping
  • Fragment Linking and Growing
  • Medicinal Chemistry Transformations
  • Combinatorial Library Enumeration
  • Multi-Fragment Search
  • Ligand Hybridization (BREED)
  • Custom Fragment Libraries

Structural Bioinformatics

  • Multiple Sequence and Structure Alignment
  • Annotate 3D Properties onto Sequences
  • Create and Search Protein Family Databases
  • Mine Structural Data
  • Analyze Conserved Residues
  • Generate Clustered Phylogenetic Trees
  • Antibody and TCR Structural Databases

Molecular Simulations

  • Molecular Mechanics and Dynamics
  • Automated Structure Preparation
  • Free Energy Calculations
  • Flexible Alignment of Multiple Molecules
  • Conformational Analysis – LowModeMD
  • Torsion Scan and Analysis
  • QM-Based NMR, IR and VCD Spectra

Peptide Modeling

  • Macrocyclic and Linear Peptides
  • Identify Peptide-Protein Contacts
  • Conformational Searching
  • Enumerate Non–Natural Peptide Libraries
  • Structure-Based Peptide Design
  • Optimize Peptide Properties
  • Peptide Docking

Structural Biology

  • Plot Electron Densities and Difference Maps
  • Display Crystal Lattices and Contacts
  • Prediction of Water Positions
  • Electron Density-Guided Docking
  • Create Aligned Protein Family Databases
  • Homology Modeling for Molecular Replacement
  • Health-Check of Protein Structures

Cheminformatics and QSAR

  • 400+ 2D and 3D Molecular Descriptors
  • pKa Prediction and Protomer Generation
  • Linear QSAR/QSPR
  • Bayesian Classification / Machine Learning
  • MOEsaic – Matched Molecular Pairs
  • Focused Combinatorial Library Design
  • Chemical Similarity, Diversity and Clustering

Customization and Deployment

  • Laptop – Cluster – Cloud – Pipeline
  • Windows – Linux – macOS
  • Integrated Programming Environment (SVL)
  • 3rd Party Software Integration
  • Custom Applications and User Profiles
  • Web Integration, Web Services, API
  • HTTP Listener for Remote Control

PSILO® - Structure Database

  • RCSB Compliant Repository
  • Browser Interface – 3D Visualization
  • Automated Project Database Curation
  • 3D Interaction Search and Statistics
  • Pocket Similarity Search
  • Protein Structure Alignment
  • Standard IT Infrastructure


Medicinal Chemists



Computational Chemists


CSD - Mogul - Gold

Omega - ROCS - OEB Files

Amber Molecular Dynamics - TI

Quantum Mechanics

Pipeline Workflows

FlexX Docking

Molecular Dynamics

Quantum Mechanics



DirectFF / TEAM Forcefield

SCM Quantum Mechanics


Marvin Sketch

ChemDraw Sketcher

Quantum Mechanics