SWORD -i <TARGET.pdb>
We also consulted a newly developed SWORD2 web server15 for analyzing two
particularly large targets with elaborate domain architecture - T1165
and T1169. The SWORD /SWORD2 programs were used in CASP for the first
time and proved to be especially helpful (in fact, the only option) for
large structures with more than 1200 residues.
If the structure parsers agreed on domain boundaries, the consensus
definition was adopted. If the programs disagreed, domain boundaries
were defined upon visual inspection, evolutionary analysis (seeStep 3 ), and /or functional information received from
experimentalists.
Alternative domain definitions were considered for cases where certain
regions of proteins were involved in domain swaps.