Binding-Site Conservation

The script to generate this image is included in OpenStructure (examples/demos/conservation.py)

Scientific Background

This script shows how to integrate data from different domains to answer a specific scientific question. By mapping the column-wise conservation of a multiple-sequence alignment onto the molecular surface, we confirm the hypothesis that the binding site of the SH2 domain is more conserved than the rest of the protein.

The Script

from ost.seq import alg
scene.RemoveAll()
#---------------------------------------------------------------------
# Loading structure and alignment
#---------------------------------------------------------------------
m=io.LoadPDB('data/sh2.pdb')
mp=m.Select('ishetatm=false')
aln=io.LoadAlignment('data/sh2.aln')
aln.AttachView(0, mp)
aln.SetSequenceOffset(0, 1)
#---------------------------------------------------------------------
# Calculate conservation of alignment
# First we set all properties to zero, then let alg.Conservation assign the
# conservation scores to the residues
#---------------------------------------------------------------------
alg.Conservation(aln)

#---------------------------------------------------------------------
# Setup Graphical Objects for Rendering
#---------------------------------------------------------------------
g=gfx.Entity('SH2', m)
s=io.LoadSurface('data/sh2.vert')
gs=gfx.Surface('SH2-surf', s)
scene.Add(gs)
scene.Add(g)
scene.CenterOn(g)

s.Attach(mp.Select('ishetatm=false'), 8.0)

gr=gfx.Gradient()
gr.SetColorAt(0.0, gfx.Color(0.1, 0.1, 0.8))
gr.SetColorAt(1.0, gfx.Color(0.8, 0.1, 0.1))

gs.ColorBy('cons', gr, 0.8, 1.0,
           mol.Prop.Level.RESIDUE)
g.SetRenderMode(gfx.HSC,
                m.Select('ishetatm=false'))
g.SetRenderMode(gfx.CUSTOM,
                m.Select('ishetatm=true'))
g.SetColor(gfx.YELLOW, 'ishetatm=true')

#---------------------------------------------------------------------
# Create alignment viewer and show it on the screen
#---------------------------------------------------------------------
seq_viewer=gui.SequenceViewer()
seq_viewer.AddAlignment(aln)
seq_viewer.Show()

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