One use of Multidomain Assembler is to set up comparative modeling and concatenation of existing structures to generate a full-length model of a multidomain protein. However, even without model-building, the byproduct is also useful: a visual summary of the structures available for a query sequence, optionally filtered by criteria such as BLAST score and % identity, laid out horizontally in approximate N→C order relative to the query. Overlapping hits are stacked vertically, and segments without structural coverage are indicated with spheres. By default, the multiple sequence alignment of the hits to the query is also displayed.

The figure shows the results of command:
    mda p08648 ~/Desktop/MDA limit 4 percent 50
with sequence mismatches in red and molecules other than the hit chains in blue. Text and pointers have been added with 2D Labels.

Multidomain Assembler is described in a paper.

The image shows tetramers of influenza neuraminidase (Protein Data Bank entry 3k3a) styled as flowers. Three tetramers are colored pink, with a central metal ion in white and nearby residues in yellow, and a fourth tetramer is colored green to resemble leaves. Each monomer or “petal” is a six-bladed β-propeller. (More samples...)