PLII-Atlas

Author: Cristian Fernandez Lopez

PDB-CAT

Author: Ariadna Llop-Peiró and Santi Garcia‑Vallvé

PDB-CAT aims to automatically categorize the mmCIF PDB structures based on the type of interaction between atoms in the protein and the ligand, and checking for any mutations in the sequence.

Llop-Peiró A, Trujillo-De León S, Pujadas G, Garcia-Vallvé S, Gimeno A. PDB-CAT: A user-friendly tool to classify and analyze PDB protein-ligand complexes. Protein Sci. 2025 Dec;34(12):e70379. doi: 10.1002/pro.70379

VHELIBS

Author: Adrià Ceretó-Massagué and Said Trujillo De León

A modern web port of VHELIBS, the Validation Helper for LIgands and Binding Sites: analyse PDB/UniProt structures for RSR, RSCC, occupancy and R-free quality, browse results with interactive filters, and inspect ligands and their electron density in an in-browser Mol* 3D viewer.

Cereto-Massagué A, Ojeda MJ, Joosten RP, Valls C, Mulero M, Salvado MJ, Arola-Arnal A, Arola L, Garcia-Vallvé S, Pujadas G. The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites. J Cheminform. 2013 Jul 29;5(1):36. doi: 10.1186/1758-2946-5-36.

pICkIT

Author: Said Trujillo De León and Santi Garcia‑Vallvé

A Python tool for analyzing and visualizing protein–ligand interaction matrices, featuring stacked and non-stacked bar charts, interactive plots, subpocket-aware residue coloring, ...