You are reading the documentation for version 1.3 of ProMod3.

Changelog

Release 1.3.0

  • Apply Apache Version 2.0 License to the project
  • 2010 Dunbrack rotamer library has been replaced by an own backbone dependent rotamer library. All scripts required to reproduce the data are in extras/data_generation/rotamer_library
  • Penultimate rotamer library has been replaced by an own backbone independent rotamer library. All scripts required to reproduce the data are in extras/data_generation/rotamer_library
  • SampleMonteCarlo function moved to Python. This makes it possible to provide sampler/closer/scorer/cooler objects implemented in both, Python and C++
  • Action script for sidechain modelling
  • Allow sequence profiles as input for build-model action script.
  • Recipe for Docker / Singularity container
  • Check peptide bonds when building a RawModel. Treat as gap if bond is stereochemically problematic despite being in sequence.
  • Several minor bug fixes, improvements, and speed-ups

Release 1.2.0

  • Graph optimizer has been separated from the sidechain module and can now be used for arbitrary optimization problems. Available optimization algorithms are TreePack, AStar and MonteCarlo.
  • Make it possible to distinguish between the scores of a loop towards a constant environment (external scores) and the scores within the loop itself (internal scores).
  • Most scores based on pairwise interactions are now pairwise decomposable.
  • Disconnected loops at several locations can be scored at once.
  • Avoid the usage of the DSSP executable and use the OpenStructure internal secondary structure assignment instead.
  • Allow to decide whether the CB atom belongs to the actual rotamer or to the constant frame in sidechain optimization. This can be useful in design questions, where the identity of a rotamer is not given and you want to allow glycine or alanine.
  • The naming of the entries in the StructureDB is not strictly limited to 4 letter codes anymore, arbitrary strings can be used instead.
  • Adding coordinates to the StructureDB does not require external tools anymore (msms, dssp etc.), internal implementations are used instead.
  • The data that is stored in a StructureDB can be controlled at initialization, everything except the sequence and the actual coordinates is optional.
  • Entries in the StructureDB can be removed again.
  • Allow to search positions of arbitrary copies in DynamicSpatialOrganizer by providing RT operators.
  • Several minor bug fixes, improvements, and speed-ups

Release 1.1.0

  • Updated dependencies: need Eigen 3.3.0 and OST 1.7
  • Changes in modelling pipeline: remove clashing loop candidates early, new scores using sequence / structure profiles, new scoring weights, subrotamer optimization to reduce ring punches, and improved handling of ligands
  • Improved build-model action to generate oligomeric models, input multiple files, and allow for residue offsets into structure files
  • Improved computational runtime of relevant operations in pipeline (CCD, scorers, backbone list operations), superpositions and loop candidate clustering
  • High-level functionality moved consistently to modelling module
  • New modelling algorithms: rigid blocks to compare structures and improved fragment sampling for de novo modelling
  • New rotamer graph solvers for sidechains: AStar and Monte Carlo
  • Refactored backbone scoring to simplify extensions
  • Added all atom scoring with possibilities to reconstruct sidechains for selected loops, reconstruct hydrogens and minimize energy with MM
  • Refactored backbone list to speed it up
  • Added runtime profiling for developers
  • Several minor bug fixes, improvements, and speed-ups

Release 1.0

  • Initial release of ProMod3 for use in productive instances of SMNG

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