JOY

JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and help understand the conservation of amino acids in their specific local environments. JOY requires a series of datafiles containing information about secondary structures, solvent accessibility and hydrogen bonding. These are produced automatically from a PDB file by supporting programs. These programs include hbond to assign hydrogen bonds, psa to calculate solvent accessibility and sstruc to assign secondary structures.