Modeller Comparative
is an interface to
Modeller
for comparative (“homology”) modeling
of proteins and protein complexes.
The example shows modeling the human (shades of blue)
from the mouse (brown and tan) complex of programmed death-1 (PD-1)
with its ligand PD-L2,
PDB 3bp5.
Comparative modeling requires a template structure and a
target-template sequence alignment for each unique chain.
The sequences of human PD-1 and PD-L2 targets were fetched from
UniProt
and associated with the corresponding chains in the template structure, see
model-pdl-setup.cxc.
(Pairwise or multiple sequence alignments could have been used, but in this case,
the template structure was simply associated with the target sequence.)
Sequence-structure association shows mismatches in the
Sequence
Viewer: pink boxes for sequence differences between mouse and human,
and gray outlines around the parts missing from the structure.
Three models were made with with default settings
(other than the number of models), and the best-scoring model
is shown. Two positions where sequence differences
change the interfacial H-bonds are displayed.
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