Klausen MS, Anderson MV, Jespersen MC, Nielsen M, Marcatili P.
LYRA, a webserver for lymphocyte receptor structural modeling.
Nucleic Acids Research. 2015;43(Web Server issue):W349-W355. doi:10.1093/nar/gkv535.
The accurate structural modeling of B- and T-cell receptors is fundamental to
gain a detailed insight in the mechanisms underlying immunity and in developing
new drugs and therapies. The LYRA (LYmphocyte Receptor Automated modeling) web
server implements a complete and
automated method for building of B- and T-cell receptor structural models
starting from their amino acid sequence alone. The webserver is freely available
and easy to use for non-specialists. Upon submission, LYRA automatically
generates alignments using ad hoc profiles, predicts the structural class of
each hypervariable loop, selects the best templates in an automatic fashion,
and provides within minutes a complete 3D model that can be downloaded or
inspected online. Experienced users can manually select or exclude template
structures according to case specific information. LYRA is based on the
canonical structure method, that in the last 30 years has been successfully used
to generate antibody models of high accuracy, and in our benchmarks this approach
proves to achieve similarly good results on TCR modeling, with a benchmarked
average RMSD accuracy of 1.29 and 1.48 Å for B- and T-cell receptors, respectively.
To the best of our knowledge, LYRA is the first automated server for the
prediction of TCR structure.