addlinks.pl                  Adds a link before every line that has '(.*) show' in a .ps file. Basically, this program adds kewl code to the .ps files, so that when they are converted to .pdf 
files, one gets kewl links.
delphi2uhbd4linux            converts Delphi binary output grid to uhbd ascii format grid.  Precompiled version assumes grids computed unde SGI Irix.
delphi2uhbd.f
do_pipsa_UHBD2APBS           pipsa 2.0 script to compare UHBD grids and APBS grids (supposes that grids have the same spacing and origin and size)
do_pipsa_uho2pqr             Script to convert UHBD output to pqr
getnames.sh                  Downloads names, long names, gene definitions from the SWISS-PROT database for the proteins
grid2insight                 Converts GRID/UHBD format grid file to InsightII readable file
grid2insight.f
gridinfo                     Gets information from the UHBD grid
gridinfo.f
highlight_kin_groups         Highlights different groups of proteins in different colours
highlight_kin_groups.f
highlight_kin_points         Highlights proteins in red
highlight_kin_points.f
insightII.HydrSurface.in     Infile for the InsightII used to produce Hydrophobic Surfaces in .wrl 
insightII.electSurface.in    Infile for the InsightII used to produce Electrostatic Surfaces in .wrl
malign3d.2.sh                Aligns the sequences to the TEMPLATE.pdb sequence, using modeller and modeller.2.in script
malign3d.pl                  Runs modeller 6 to create 3D multiple alignment of all the proteins in pdbs directory
malign3d.sh                  Aligns the sequences to the TEMPLATE.pdb sequence, using whatif
malign3d.whatif.in           Script used by malign3d.sh
mkElecSurface.sh             Creates .wrl files that represent electrostatic surfaces. UHBD calculations should be done before the script is executed.
mkHydrSurface.sh             Creates .wrl files that represent hydrophobic surfaces. GRID calculatoins should be done before the script is executed.
mktree.sh                    Creates the tree from the similarity matrix - prototype to do_pipsa_phylip
modeller.2.in                Script used by the modeller 4 in malign3d.2.sh program
orient.sh                    Alignning the proteins using ORIENT command from the modeller. _very_ inaccurate
pqr2qcd                      Converts PQR format to UHBD readable QCD format
pqr2qcd.f
uho2pqr                      Converts UHBD output to pqr
uho2pqr.f
