Select Parameters Please provide entries via file upload or PDB id. The latter can be optionally followed by the chain identifier, e.g. 3hvgA selects chain A of PDB entry 3hvg.
Sample input: to align the HIV-1 protease and human beta-secretase enter 1aid and 3hvgA in the two PDB code fields.

Reference: full text article
ALADYN: a web server for aligning proteins by matching their large-scale motion
R. Potestio; T. Aleksiev; F. Pontiggia; S. Cozzini; C. Micheletti
Nucleic Acids Research 2010; doi: 10.1093/nar/gkq293