Modelling of a T-cell Receptor V-alpha Domain: Sequence Alignment
More difficult, therfore less reliable, second attempt to model the TCR after the two known structures of T-cell receptors (an earlier model was based on VL and VH templates, problems in the CDR2 region
V-alpha templates - In contrast to the target sequence, the template structures do not have Pro in L8 Comparison of the surrounding sequence with VL kappa domains and the TCR V-beta domains suggests that this proline might be in cis-conformation. This segment of V-alpha was therfore modelled after a V-beta template
CDR2 and CDR3 loops: no template of appropriate length -> loop search or generation by conformational search, simulated melting and annealing.