SPRUCE 1.5.0

Spring 2022

New Features

  • Spruce has been enhanced to perform standardization and a filter checks before Spruce preparation.

    The following are detected and fixed:
    • invalid component names

    • invalid residue states

    • invalid metal bonds

    The following are detected and fail the structure:
    • invalid CRYST1 from header file

    • low overlap between the electron density map and the structure

    • invalid sequence alignment

    • blank Chain IDs

    • invalid alternate locations

  • Spruce has been enhanced to perform checks on the generated design unit after running Spruce preparation.

    Issues detected and reported include:
    • partial side chains

    • missing loops

    • implicit hydrogens

    • incorrect partial charges

    • termini that are not capped properly

    • heavy atoms overlapping with each other

    • broken chains

  • A new command line option -enum_pockets has been added. When enabled it automatically detects pockets and generates design units from them.

Minor Bug Fixes

  • An issue with the value of the parameter -min_align_score not being properly respected has been fixed.

Spruce TK 1.5.0

New features

Major bug fixes

  • A bug that caused memory leaks in OEBio TK has been fixed.

Minor bug fixes

  • An issue was fixed in OEBuildLoops to allow better sequence alignment for peptides.

  • An issue was fixed in OEBuildLoops where free amino acids, as co-factors or ligands, were incorrectly included in sequence alignments and causing mismatched alignments to the SEQRES.

  • An issue was fixed in OEExtractBioUnits to be able to lower the minimum sequence alignment score threshold.