The PLIP Protein-Ligand Interaction Profiler has been updated.

According to the Changelog

1.2.0

• Support for DNA and RNA as ligands__
• Detection of metal complexes with proteins/ligands, including prediction of geometry__
• Extended result files with detailed information on binding site residues and unpaired atoms__
• Support for zipped and gzipped files__
• Rich verbose mode in command line with information on detected functional groups and interactions
• Automatic fixing of common errors in custom PDB files
• Refined binding site selection
• Better overall performance
• Initial test suite for metal coordination
• Classification of ligands
• Improves detection of aromatic rings and interactions involving aromatic rings
• Single nucleotides and ions not excluded anymore as ligands
• Generation of canonical smiles for complete (composite) ligands
• Generation of txt files is now optional
• Basic support for PDBQT files
• Correct handling of negative chain positions of ligands
• Improved check for valid PDB IDs
• Fixes several bug

The web service includes all the updates and integrates BioLip for flagging biologically relevant interactions. Since ligand molecules (e.g., Glycerol, Ethylene glycol) are often used as additives (i.e., false positives) for solving the protein structures, not all ligands present in the PDB database are biologically relevant.