CogniChem Application

Structure QC Report

Grade the geometry of predicted or experimental protein models: Ramachandran and rotamer outliers, atomic clashes, cis-peptides, Cβ deviation, and ligand bond geometry. A fast check before docking, MM-GBSA, or model training.

Job name

Resource

Estimated minimum cost: $—

Examples

Input

Upload 1–200 predicted, designed, or experimental models (PDB or CIF), up to 5,000 protein residues each. Each model is graded on its own (first model, selected chains), coordinates unchanged. Select a file to preview it.

Models

or drop files here

QC options

Heavy atoms are graded against CogniChem-defined Ramachandran regions, canonical side-chain rotamers, van der Waals overlap, peptide ω, and ideal Cβ placement. Each ligand's bonds and angles are compared with an MMFF94-minimized copy of itself. Every metric is marked pass, warn, or fail against the thresholds below; values do not numerically match MolProbity.

ChainsBlank grades every chain.

Grade ligand bond and angle geometry (ligands are always clash-checked)B-factors are pLDDT (flag low-confidence residues instead of penalizing them)

Thresholds and cutoffs

Leave a field empty to use the default shown in it. A metric at or above its warn value is a warning and at or above its fail value a failure; Ramachandran favored grades low values (at or below).

Clashscore (per 1,000 atoms)

Ramachandran outliers (%)

Ramachandran favored (%)

Rotamer outliers (%)

Cβ deviation outliers

Non-Pro cis-peptides

Twisted ω

Ligand geometry outliers

What counts as one outlier

Clash overlap (Å)Default 0.4 (0.2–1)Cβ deviation (Å)Default 0.25 (0.1–1)Cis ω window (°)Default 30 (10–60)ω twist (°)Default 30 (10–60)Ligand |Z| outlierDefault 4 (2–10)