ProteinIQ for structure validation

Validate structures before you publish

Assess predicted and experimental protein structures using MolProbity, Ramachandran analysis, and structural comparison tools.

MolProbity

All-atom validation with clashscore, Ramachandran, and rotamer analysis. The gold standard for structure quality.

DockQ

Assess docking model quality with a single score. Evaluate protein-protein complex predictions.

USAlign

Universal structure alignment for proteins, RNA, and complexes. Calculate TM-score and RMSD.

FoldSeek

Ultra-fast structure search. Find similar proteins across databases in seconds.

RMSD Calculator

Calculate root-mean-square deviation between structures. Compare predicted vs experimental coordinates.

Ramachandran Plot

Visualize backbone dihedral angles to assess structure quality and identify outliers.

Why researchers choose ProteinIQ

MolProbity and Ramachandran analysis provide confidence-independent validation

Predicted structures lack quality metrics like experimental structures

All validation tools run in your browser—no setup required

Running validation tools locally requires multiple installations

FoldSeek searches structure databases in seconds

Comparing structures across databases is tedious and slow

PROPKA predicts ionization states with a simple upload

pKa predictions needed for MD but tools are hard to use

How it works

Professional structure validation and quality assessment using industry-standard tools. Validate backbone geometry with Ramachandran plots, check all-atom contacts with MolProbity, predict pKa values with PROPKA, and compare structures with USAlign and FoldSeek.

Upload structure

Provide PDB file or fetch from RCSB

Validate geometry

MolProbity checks clashes, rotamers, and more

Analyze backbone

Ramachandran plot shows phi/psi distribution

Compare & search

Find similar structures with FoldSeek or USAlign