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.