Related tools
RMSD calculator
Calculate Root Mean Square Deviation (RMSD) between protein structures. Compare a reference PDB against multiple structures with automatic Kabsch alignment.
DockQ
Assess docking model quality by comparing predicted complexes against native references. DockQ v2.1.3 supports protein, nucleic-acid, and supported small-molecule interfaces with faithful native metrics.
PoseBusters
PoseBusters validates generated or docked molecular poses with chemically and structurally grounded quality checks for molecular geometry, intermolecular interactions, and optional reference-pose agreement.
MolProbity
Validate protein structure quality with all-atom contact analysis, Ramachandran plots, rotamer assessment, and geometry checks.
PDBsum
Generate a downloadable PDBsum structural summary report archive for a single protein structure.
AllMetal3D
Predict metal and water binding sites in protein structures using 3D convolutional neural networks (AllMetal3D + Water3D).
LocScale
LocScale performs physics-informed local sharpening of cryo-EM density maps using half-maps or full MRC/MAP volumes, with optional mask and reference-map inputs.
SuperWater
Predict protein hydration sites from a structure using a diffusion model with ESM features and a confidence-filtering head.
DSSP
Assign protein secondary structure using the DSSP algorithm. The gold standard for hydrogen bond-based structure assignment from coordinates.
Radius of gyration
Calculate the radius of gyration (Rg) for protein structures from PDB files. Supports multiple chains and atom selection options.