MOE

Computer-aided molecular design for small molecules, peptides, and biologics with 3D visualization, structure-based design, and virtual screening.

Overview

MOE (Molecular Operating Environment) is an integrated computer-aided molecular design platform developed by Chemical Computing Group. It is designed to support drug discovery workflows across small molecules, peptides, and biologics, and serves as a common platform for medicinal chemists, biologists, crystallographers, and computational chemists.

MOE covers the full range of structure-based and ligand-based design activities, from 3D molecular visualization and virtual screening through to molecular simulations, cheminformatics, and structural bioinformatics. The platform also includes MOEsaic for SAR exploration and integrates with PSILO, a protein structure repository.

3D Molecular Visualization

Graphical interface for molecular visualization
Active site detection and analysis
Molecular surfaces and electron density display
Visualization of non-bonded interactions
Publication-quality image and movie export
GPU-accelerated 3D stereo graphics
Support for mixed virtual reality and 3D printing

Structure-Based Design

Streamlined interface for ligand design
Interactive ligand design within the binding pocket
Protein-ligand interaction diagrams
Prediction of water sites and energetics
Induced-fit docking
Fragment linking, growing, and replacement

Antibody and Biologics Design

Structure-based protein engineering
Assessment of liabilities and developability
Optimization of affinity, stability, and solubility
High-throughput antibody modeling
Generation of virtual libraries
Protein docking and epitope mapping
Modeling of ADCs and fusion proteins

MOEsaic – SAR Explorer

SAR and SPR visualization
Free-Wilson compound suggestions
Matched molecular pairs analysis
R-group analysis and profiling
Substructure and similarity search
Design of novel virtual compounds
Documentation and sharing of design sessions

Ligand-Based Design

Conformation generation and clustering
Alignment and superposition of small molecules
Pharmacophore elucidation and screening
QSAR model generation using MOE descriptors
Torsion profiles for conformation analysis
Combinatorial library enumeration

Protein, DNA/RNA Modeling

Visualization of proteins, patches, and interfaces
Prediction of 3D protein structure from sequence
Building of DNA/RNA models
Exploration of mutations and rotamers
Molecular dynamics simulations
Loop and linker searching and sampling
Protein-protein docking

Virtual Screening

3D pharmacophore screening with 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 via BREED
Custom fragment libraries

Structural Bioinformatics

Multiple sequence and structure alignment
Annotation of 3D properties onto sequences
Creation and searching of protein family databases
Mining of structural data
Analysis of conserved residues
Generation of 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 using LowModeMD
Torsion scan and analysis
QM-based NMR, IR, and VCD spectra

Peptide Modeling

Modeling of macrocyclic and linear peptides
Identification of peptide-protein contacts
Conformational searching
Enumeration of non-natural peptide libraries
Structure-based peptide design and property optimization
Peptide docking

Structural Biology

Plotting of electron densities and difference maps
Display of crystal lattices and contacts
Prediction of water positions
Electron density-guided docking
Homology modeling for molecular replacement
Health-check of protein structures

Cheminformatics and QSAR

Over 400 2D and 3D molecular descriptors
pKa prediction and protomer generation
Linear QSAR and QSPR modeling
Bayesian classification and machine learning
Matched molecular pairs via MOEsaic
Focused combinatorial library design
Chemical similarity, diversity, and clustering

PSILO – Protein Structure Repository

RCSB-compliant repository with browser interface and 3D visualization
Automated project database curation
3D interaction search and statistics
Pocket similarity search and protein structure alignment
Storage of both public and proprietary structures
Electron density map visualization and sequence annotation display
On-the-fly superposition and interactive 3D viewer with storyboard
Secure cloud hosting certified to ISO-27001

Additional Integrated Capabilities

Antibody developability assessment including ensemble-based property calculations, liability hot spot detection, PTM detection, and standardized 2D protein patch maps
Automated SAR reporting with MMPs, R-group deconvolution, and scaffold suggestions
Assay data management covering sample registration, inventory tracking, liquid handling qualification, assay data capture, QA/QC analysis, and FAIR-compliant data storage
Integration with third-party scientific software including LiveDesign, PipelinePilot, and Spotfire
No-code system integration with end-to-end workflow security