ProteinIQ for molecular dynamics

Run molecular dynamics in the cloud

Run advanced MD simulations and steered dynamics to understand protein behavior and conformational changes over time.

OpenMM

GPU-accelerated molecular dynamics simulations. Run nanosecond-scale simulations with AMBER and CHARMM force fields.

AlphaFlow

Sample protein conformational ensembles using flow-based generative models. Explore dynamics without expensive MD.

PDB2PQR

Prepare structures for electrostatics calculations. Add hydrogens, assign charges, and optimize H-bond networks.

PROPKA

Predict pKa values for ionizable residues. Essential for correct protonation states in MD simulations.

PDB Fixer

Prepare structures for simulation. Fix missing atoms, add hydrogens, and repair common PDB issues.

DSSP

Calculate secondary structure assignments from coordinates. Track structural changes during simulations.

Why researchers choose ProteinIQ

Cloud-based MD runs on powerful GPUs—no cluster management

MD simulations require specialized HPC clusters and expertise

Automated preparation pipeline handles system setup

System setup (solvation, ionization, minimization) is tedious

Built-in analysis tools for RMSD, RMSF, and contact maps

Trajectory analysis requires programming skills

Offload to cloud—free your workstation for other tasks

Long simulations tie up local resources for days

How it works

Advanced molecular dynamics simulations to study protein motion, conformational changes, and dynamic behavior over time using state-of-the-art simulation engines.

Upload structure

Provide starting PDB structure for simulation

System setup

Automated solvation, ionization, and minimization

Run simulation

Execute MD on cloud GPUs with progress tracking

Analyze trajectory

Visualize dynamics, compute RMSD/RMSF, export data