Chiron rapidly minimizes steric clashes in protein structures using short discrete molecular dynamics (DMD) simulations. Gaia evaluates the quality of a protein structure against multiple criteria benchmarked against high-resolution crystal structures.
Submit a protein structure (by PDB ID or file upload)
Choose Chiron for clash minimization or Gaia for structure validation
Wait for background processing (typically a few minutes)
Review results: clash scores, structural metrics, and downloadable PDB files
Optionally refine side chains or submit to Chiron from Gaia results
Identify and resolve severe atomic overlaps that arise in homology models, low-resolution structures, and noisy coordinate sets using short discrete molecular dynamics simulations.
Evaluate protein structure quality across multiple metrics: steric clashes, hydrogen bond satisfaction, surface area, void volumes, bond geometry, and side chain integrity. Benchmark against high-resolution crystal structures.
Submit by providing a 4-character PDB ID or uploading a PDB file. Optionally constrain side chains.
| Parameter | Description |
|---|---|
| pdbid | 4-character PDB code (e.g. 4HHB) |
| queue | chiron or gaia |
| constrain | Harmonic side chain constraints |
| mlcs | Include small molecules |