PLIP v1.2.0

• 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 bugs

PLIP v1.1.1

• Detailed information on binding site residues in XML files
• Improved extraction of binding site residues
• Information whether halogen bonds are made with side- or main chain of protein

PLIP v1.1.0

• Folder structure and setup.py for automatic installation using pip
• H-Bond Donor Prioritization (see documentation for details)
• Adds separate changelog
• Updated documentation and citation information
• Reduction of blacklist usage
• Information on excluded ligands in result files

PLIP v1.0.2

• Automatic grouping of composite ligands (e.g. polysaccharides)
• Proper handling of alternative conformations in PDB structures
• Exclusion of modified residues as ligands
• Improved detection of hydrogen bonds
• Prioritization of hydrogen bonds
• Adds atom type description in the output files
• Basic support for usage on Windows (without multithreading)
• Option to turn multithreading off by setting maxthreads to 0
• Improved detection of hydrogen bond donors in ligands
• Adaption of standard parameters
• Fixes a bug in PyMOL visualization script leading to missing or wrong interactions with pseudoatoms
• Fixes a bug leading to duplicate or triplicate detection of identical pi-cation interactions with guanidine
• Adds now unit tests
• Small changes to existing unit tests for new features

PLIP v1.0.1

Changes

• Option to change detection thresholds permanently or for single runs
• Option to (de)activate output for images, PyMOL session files and XML files
• Changed standard behaviour to output of RST report only
• Information on sidechain/backbone hydrogen bond type
• Sorted output
• Detection of more flavors of halogen bonds
• Fixed bug leading to duplicate interactions with quartamine groups