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
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 %