Capabilities

• Monte Carlo simulations in NPT, NVT, and μVT ensembles
• OPLS force fields for organic molecules and biomolecules
• Semi-empirical QM methods: AM1, PM3, PDDG/PM3
• Energy minimisation and normal mode analysis
• Free energy perturbation and thermodynamic integration
• Conformational searching and geometry optimisation

Capabilities

• Protein-ligand binding free energy calculations
• Explicit and implicit solvent models
• Residue-based cutoffs for efficient sampling
• Z-matrix internal coordinate moves
• Solute-solvent and solute-solute energy decomposition
• Compatible with OPLS-AA force fields

Capabilities

• De novo ligand growth in protein binding sites
• Virtual screening of combinatorial libraries
• Docking with scoring and ranking
• Lead optimisation guided by FEP calculations
• Fragment-based drug design support
• Protein structure preparation and editing

Capabilities

• Relative and absolute binding free energies
• Free energies of hydration and solvation
• Thermodynamic integration protocols
• Bennett Acceptance Ratio (BAR) analysis
• Alchemical transformations between ligands
• Industry-standard accuracy for lead optimisation

Capabilities

• OPLS-AA: all-atom parameters for organic molecules
• OPLS-AA/L: improved backbone parameters for proteins
• Coverage of 100+ functional groups
• Validated against experimental liquid properties
• Compatible with BOSS, MCPRO, and major MD packages
• Custom parameterisation tools for novel compounds

Capabilities

• Interactive 3D molecular viewer in the browser
• Ball-and-stick, space-fill, ribbon, and surface modes
• Trajectory playback for MD and MC simulations
• Electron density and electrostatic potential surfaces
• Protein-ligand binding mode visualisation
• Export publication-quality images and animations