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EncoMPASS

Source code for building the EncoMPASS database

Contributors

Antoniya A. Aleksandrova
Edoardo Sarti
Lucy R. Forrest

Release Notes & Current Updates

Current Updates

Structure Retrieval

  • added information about processing and decision-making steps to the header of each structure

Structure Alignment

  • TMs of all sequence-related chains are considered when deciding which comparisons to make
  • 1 & 2 TM chains have a different set of rules from larger chains, which includes a condition about the size of the domains on either side of the membrane

Symmetry Algorithms Used

  • CE-Symm v2.2.2
  • QuatSymm v2.2.2
  • SymD v1.6
  • AnaNaS v1.1 (not currently used for analysis, but available)

Multi-step Symmetry Selection (MSSD)

  • We've integrated QuatSymm in the MSSD procedure. We postprocess QuatSymm results to guess the specific repeat range and use the output only if the resulting symmetry has comparable RMSD and TM-score to the one reported by QuatSymm.
  • Quaternary symmetries with only 1 TM chain in a repeat are now considered acceptable and are reported.

Dependencies & Containers

PPM v2.0 is used to insert structures in the membrane if the OPM structure for the associated biological assembly is not available. For more information, please see the PPM website
MUSCLE v3.8.3 is used to align sequences. See Muscle v3 website
FrTMAlign is used to align structures. See FrTM-Align website
Symmetries are calculated with:

These dependencies can be copied to and run from a container, instructions for which are available on github