Key Features
- 1Powerful and flexible MD simulations
- 2Multiple integrators for different simulation types
- 3Support for various thermostats and barostats
- 4Enhanced sampling techniques
- 5GPU-accelerated calculations for faster results
- 1Automated topology generation and parameterization
- 2Intelligent solvent box creation and ion placement
- 3Support for membrane proteins and lipid bilayers
- 4Custom ligand parameterization and integration
- 1RMSD, RMSF, and radius of gyration calculations
- 2Hydrogen bond and contact analysis
- 3Principal component analysis and essential dynamics
- 4Free energy calculations and binding affinity estimation
- 1Automated data organization and storage
- 2Version control for simulations and analyses
- 3Reproducible workflows and sharing capabilities
- 4Efficient handling of large trajectory files
Interactive 3D Molecular Viewer
Visualize molecular structures with our powerful 3D viewer. Explore proteins, ligands, and complexes with multiple visualization styles and interactive controls.
- Multiple visualization styles (cartoon, stick, sphere, surface)
- Interactive rotation, zoom, and translation controls
- Various coloring schemes to highlight structural features
- Direct access to PDB structures from the Protein Data Bank
Specialized Applications
- Binding free energy calculations (MM/PBSA, MM/GBSA)
- Residence time estimation for drug candidates
- Binding pathway elucidation with enhanced sampling
- Structure-activity relationship insights
- Identification of cryptic binding sites
- Allosteric pathway mapping
- Conformational free energy landscapes
- Functional motion and dynamic domains
- Automated membrane protein embedding
- Multiple lipid composition support
- Membrane-protein interaction analysis
- Transport and channel function studies
- Stability assessment of engineered proteins
- Mutation impact prediction
- Functional property optimization
- De novo design validation
Complete Workflow
From system preparation to analysis, our platform guides you through every step of the molecular dynamics process
Structure Preparation
Start with a protein structure from our structure prediction pipeline or upload your own. Our system automatically checks for missing residues, adds hydrogens, and prepares the structure for simulation.
System Setup
Define your simulation environment with our intuitive interface. Choose force fields, add solvent, ions, ligands, or membrane components as needed for your system.
Simulation Protocol
Configure your simulation protocol with our template-based system. Choose from standard protocols or customize every aspect of your simulation.
Simulation Execution
Run your simulation on our high-performance computing infrastructure. Monitor progress in real-time, with automatic checkpointing and the ability to extend simulations as needed.
Analysis & Visualization
Analyze your simulation results with our comprehensive suite of tools. Generate publication-quality figures, extract meaningful metrics, and gain insights into your molecular system.