Ligora

Ligora is a molecular analysis workstation for protein-ligand interaction analysis, molecular docking, and computational chemistry workflows — built entirely on open data sources and open engines.

Features:

• Open and visualize PDB, mmCIF, mol2, SDF/MOL, XYZ, GRO and PDBQT files
• Real protein-ligand contact analysis via PLIP (hydrogen bonds, hydrophobic, salt bridges, pi-stacking, metal coordination)
• Molecular docking with AutoDock Vina (real poses + affinities)
• GROMACS minimization and short-MD snippets
• Pocket detection, DSSP secondary structure, 2D interaction diagrams
• Ligand identity resolution via PubChem, ChEMBL and CCD
• PDB-wide search, BindingDB enrichment, UniProt/AlphaFold context
• Batch analysis, pose comparison, water-network analysis, 2D ligand editor
• Scripting console and reproducibility manifests

Everything visible runs end-to-end against real data — no placeholders, no fakes.