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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 CAMPASS. JOY can mix
structurally annotated sequences with simple sequences (with no structural
information) such as 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. |
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.