All tools

Predict molecular energies, atomic forces, atomic and spin charges, dipole vectors, stress tensors, and Hessians from coordinate-bearing molecular structures with AIMNet2 neural network potentials.

Calculate binding free energies using MM/PBSA and MM/GBSA methods for protein-ligand, protein-protein, and protein-DNA complexes. Provides detailed energy decomposition and per-residue contributions.

Run molecular dynamics simulations using the GROMACS engine with classical force fields (AMBER, CHARMM, GROMOS, OPLS). Study protein dynamics, conformational flexibility, and structural stability with production-grade MD methodology.

Analyze molecular dynamics trajectories using a ProteinIQ tool pinned to MDAnalysis 2.9.0. Calculate RMSD, residue-aggregated RMSF, radius of gyration, distance tracking, and additional trajectory observables from standard topology and trajectory files.

MDGen is a generative AI model for molecular dynamics trajectory generation. Generate physically plausible conformational ensembles from a single protein structure, enabling rapid exploration of protein dynamics without expensive MD simulations.

Calculate absolute hydration free energies (AHFE) for neutral small molecules with OpenFE and GPU-accelerated OpenMM simulations.

Run molecular dynamics, minimization, and energy calculations with OpenMM. Prepare solvated or membrane systems, use native parameter files, and configure restraints, enhanced sampling, or machine-learning potentials.

ORB v3 predicts atomistic energies, forces, stress, and confidence, with optional BFGS geometry optimization or Langevin NVT molecular dynamics.