Related tools
PLIP
Analyze noncovalent interactions in protein-ligand complex structures with PLIP, including hydrogen bonds, hydrophobic contacts, pi interactions, salt bridges, water bridges, halogen bonds, and metal complexes.
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.
ScanNet
Geometric deep learning model for predicting protein binding sites directly from 3D structure. Identifies where proteins interact with other proteins, antibodies, or disordered proteins with high accuracy, including for novel protein folds.
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.
AllMetal3D
Predict metal and water binding sites in protein structures using 3D convolutional neural networks (AllMetal3D + Water3D).
DSSP
Assign protein secondary structure using the DSSP algorithm. The gold standard for hydrogen bond-based structure assignment from coordinates.
IPSAE
Scoring function for interprotein interactions in AlphaFold2, AlphaFold3 and Boltz predictions. Calculates ipSAE, ipTM, pDockQ, pDockQ2, and LIS scores to assess protein-protein interface quality.
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.
Molecular descriptors
Compute 200+ RDKit molecular descriptors, drug-likeness rule violations, and structural fingerprints for QSAR, virtual screening, and ML workflows
MolProbity
Validate protein structure quality with all-atom contact analysis, Ramachandran plots, rotamer assessment, and geometry checks.