|Mizuguchi, K., Deane, C.M., Blundell, T.L., Johnson,M.S. and Overington, J.P. (1998) JOY: protein sequence-structure representation and analysis. Bioinformatics 14:617-623.|
What is 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. For instance, it has been recognised that a sidechain hydrogen-bonded to a main-chain amide plays an important role in stabilizing the 3D structure and is generally well conserved during evolution. Such a residue is shown in a bold-face letter in the formatted alignments. Another example is the importance of solvent inaccessible residues which are shown in UPPER-CASE letters.
What does JOY output look like?Here are some examples of annotated forms of sequence alignments in HTML, black and white PostScript and colour PostScript (you need a viewer such as ghostscript to view PostScript files). The colour PostScript may not look nice on the screen, but its colours were chosen to produce the best quality printout (at least for our printer). Click here for the key to JOY format. (This corresponds to the colour version of Fig. 1 of the paper. The key is also shown in the manual.
Where is it used?The JOY representation now constitutes an essential part of the two databases of protein structure alignments: HOMSTRAD and this, which is quite useful for comparative modelling. JOY has also been successfully used for identifying distant evolutionary relationships (see references and also the program FUGUE)..
How does it work?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. For more information, see the online manual of JOY.
OK, let me run JOYClick on the DOWNLOAD link on the left. Also try our JOY server.