OpenStructure 2.4

Release Notes

  • Add fast and flexible lDDT implementation. The new code is purely Python based, natively supports complexes and is able to score DNA/RNA. The deprecated lDDT implementation remains for consistency.
  • Add algorithms to establish one to one mappings between chains in a reference structure and a model. Chain mappings can be derived by optimizing oligomeric lDDT, RMSD or QS-score.
  • Substitution matrixes for RNA/DNA to compute alignments: seq.alg.IDENTITY and seq.alg.NUC44.
  • Add binding to DockQ ( as well as an OpenStructure specific implementation of it. Also allows to extract CAPRI specific oligo scores (fnat, fnonnat, irmsd, lrmsd etc.)
  • Reimplentation of QS-score in mol.alg.qsscore. Implements speedups and heavy caching which benefits heavy enumeration approaches in chain mapping.
  • Stereochemistry related algorithms in mol.alg.stereochemistry. Identifies clashes and non-sensible bond lengths/angles based on parameterizations from CCP4 MON_LIB.
  • Add non-polymer/small molecule ligand scoring algorithm with lDDT-PLI and symmetry-corrected ligand RMSD scores that were used in CASP15.
  • Better compression in OMF structure format.
  • Two central scoring objects to access to all OpenStructure specific scoring capabilities. Tertiary and quaternary structures and interactions, including required pre-processing of model/reference (cleanup, stereochemistry checks, chain mapping etc.) with mol.alg.scoring.Scorer. Non-polymer/small molecule ligands with mol.alg.ligand_scoring.LigandScorer.
  • Re-write of compare-structures action to include newly developed chain mapping and scores. The old action is available as compare-structures-legacy.
  • Add compare-ligand-structures action which computes lDDT-PLI and symmetry-corrected ligand RMSD scores in protein complexes.
  • Several minor bug fixes and improvements.


Download the latest version of OpenStructure.

Compilation instructions for this version can be found here.

Financial Support

Swiss Institute of Bioinformatics

Biozentrum, University of Basel