OpenStructure 2.8

Release Notes

  • heavy water (DOD) is now recognised as 'water' instead of 'non-polymer' by the compounds library.
  • Added a '--version' argument to the 'ost' executable
  • SEQRES information is now read from the entity_poly_seq category in mmCIF. The canonical as well as semi-canonical (with 3 letter-codes in bracket) SEQRES are now available from the MMCifInfo object. The (Get|Set)ReadCanonicalSeqRes (Get|Set)ReadSeqRes methods no longer exist.
  • Disabled numpy support in C++ layer to simplify build system. Some exotic OST functionality directly accessed Python numpy arrays from the C++ layer which required to compile against numpy headers.
  • Introduce GDT score which is equivalent to LGA (99.2% of CASP15 TS models score within 3 GDTTS points when compared to LGA results). Oligo/RNA support comes for free when using the ost.mol.alg.scoring.Scorer object.
  • Introduce ilDDT score in scoring.Scorer and compare-structures action. It's an all atom lDDT score which only considers interface contacts.
  • Rigid superposition based scores (RMSD, GDT) in ost.mol.alg.scoring.Scorer now use RMSD based chain mapping when scoring oligos.
  • scoring.Scorer and compare-structures action can now optionally enable peptide specific parameterizations as defined by the CAPRI community for DockQ related scores (fnat, fnonnat, irmsd, lrmsd).
  • Ligand scoring refactoring. lDDT-PLI and symmetry corrected RMSD are now completely separated and this comes with API changes. This also affects trg/mdl ligand assignment which now differs between the two. lDDT-PLI definition has been changed and slightly different results can be expected.
  • Breaking changes in compare-ligand-structures action output - run 'ost compare-ligand-structures -h' for more information.
  • Added 'full_bs_search' argument in ligand scoring. Binding sites for symmetry corrected RMSD computation are now searched by only considering polymer chains in proximity of ligands to speed up computations on large complexes. The old behavior can be restored by enabling this flag.
  • Added model contacts in lDDT. lDDT is not symmetric in a sense that added/wrong contacts in the model do not penalize the score. lDDT now comes with a flag to add such contacts, i.e. contacts between atom pairs in the model that are within the specified lDDT threshold (usually 15A), IF the respective atom pair is also present in the target.
  • lDDT-PLI can optionally use the new added mdl contacts feature. Think of nasty loops that interact with the ligand in the model which would not be penalized by classic lDDT!
  • Remove seq.alg.MATCH and seq.alg.IDENTITY preset substitution matrices
  • Enable parasail (https://github.com/jeffdaily/parasail) as drop-in replacement for naive LocalAlign/GlobalAlign/SemiGlobalAlign implementations. Must be enabled at compile time - see installation instructions.
  • Alignments in ChainMapper now use SemiGlobalAlign instead of GlobalAlign strategy in order to improve the alignment of terminal regions.
  • ChainMapper.GetMapping now uses backbone only lDDT with inclusion radius 30A as target function if nucleotide chains are present. Protein only structures still use QS-score as target function as before.
  • Remove ost.io.IoProfile.quack_mode property
  • Several bug fixes and improvements.

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Financial Support

Swiss Institute of Bioinformatics

Biozentrum, University of Basel