Sequence Independent Molecular Replacement Based on Available Database

Documentation Status CI Status Solution count SIMBAD paper


SIMBAD is a sequence independant molecular replacement pipeline developed by the group of Daniel Rigden at the University of Liverpool. SIMBAD provides an alternate strategy to identify Molecular Replacement search models in a sequence-independent manner.

This makes SIMBAD suited to:

  • Solve cases of contaminant crystallisation, and other mishaps such as mistaken identity (swapped crystallisation trays),
  • Solving unsequenced targets
  • Provide a brute-force approach where sequence-dependent search model identification could be non-trivial e.g. because of conformational diversity among identifiable homologues.

For an overview of SIMBAD, watch this video.


SIMBAD implements a three-step pipeline to efficiently identify a suitable search model in a database of known structures.

  1. SIMBAD performs a lattice search against the entire Protein Data Bank, rapidly determining whether or not a homologue exists in the same crystal form.
  2. SIMBAD screens the target data for the presence of a crystallised contaminant, a not uncommon occurrence in macromolecular crystallography. To catch for this eventuality, SIMBAD rapidly screens the data against a database of known contaminant structures. This database is compiled to include entries from ContaBase and Dimple.
  3. The final step in SIMBAD can be invoked to perform a brute-force search of a non-redundant PDB database provided by the MoRDa MR software.

The following flowchart provides a quick overview of the SIMBAD approach: