Cluster Analysis of water sites of urokinase-ligand-complexes
WatCH:
A tool for identifying conserved water sites and analyzing their
degree of
conservation using heirarchical cluster analysis of superimposed
related Protein Data Bank
structures.
- extracting water molecules from 36 aligned urokinase structures (uPA.align.pdb.tar.gz)
/home/henricsn/Program/WatCH/bin/prep_WatCH $pdb $file
urokinase.water
- running clustering program with threshold of 2.4 A
(urokinase.cluster240)
-
# Transform from absolute to relative conservation
$program"cluster2percent.pl" $number $file
$output.percent
# Transform the cluster files into PDB files for visualization
$program"cluster2pdb.pl" $file $output.pdb
$program"cluster2pdb.pl" $output.percent
$output.percent.pdb
# Determine which clusters have water molecules from the same structure
$program"check_cluster_contents.pl" -d $file
$output.samestr
# Count the number of water molecules from each structure in each
cluster
$program"check_cluster_contents.pl" -c $file
$output.strcount
urokinase.cluster240.tar
- water sites with certain occupancy in clustal analysis (urokinase.cluster240_waters.pdb.tar)
- movie of active site (1ghw) with colored water sites according to
their occupancy (1gj7-model-cluster-docked.avi):
red 80 %, yellow 70-80 %, light blue 50-70 %, dark blue 30-50 %
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