BLOGGER TEMPLATES AND TWITTER BACKGROUNDS

mardi 25 mars 2008

Docking contact pairs occurence

Docking or montecarlo procedure produce a huge number of conformation that have to be analysed. As bioinformatician we generally wrote some script to help in such task. In the present exemple, I explain how to calculate/analyse the amino acid occurence of presence at the interface, and furthermore, the occurence of particular pairs of residues in contact. All is done in the ICM package (http://www.molsoft.com/), and lead to produce 3D plot of matrice of pair contact.







The icm code (for example, not complete for clarity purpose):



#All this script is place in the loop exploring all the conformation (ie stack or trajectories)
load conf i OR load frame i
#method1 get the residues from each partnairs at the interface for a particular pose
show surface area a_1.// a_1.//
inter1=Res(Sphere(a_2.//* a_1.//* 4.) & Acc(a_1./*))
show surface area a_2.// a_2.//
inter2=Res(Sphere(a_1.//* a_2.//* 4.) & Acc(a_2./*))

#method2 get the pairs residues at the interface for a particular pose
t=Area(a_2./A, a_1./A)
read column group name="aa" input=s_out

#given the list of pair, creating the matrix of occurence
RI12=Matrix(72,50,0)
for j=1,Nof(aa)
y=Integer(Name(aa.2[j])[3:Sz])
x=Integer(Name(aa.3[j])[3:Sz])
RI12[x,y]=RI12[x,y]+1
endfor

#Zscore/normalisation of the matrix
Ntot=Sum(Sum(RI12))
for i=1,Nof(RI12[1,?])
for j=2,Nof(RI12[?,1])
nobsi=Sum(RI12[?,i])
fj=Sum(RI12[j,?])/Ntot
ntheoij=nobsi*fj
nobsvij=RI12[j,i]
zij=(nobsvij-ntheoij)/Sqrt(ntheoij)
ZRI12[j,i]=zij
endfor
endfor
#normal plot
plot area RI12 grid link ds

#3D plot
x=Rarray(50,Min(ZRI12),Max(ZRI12))
y=Rarray(72,Min(ZRI12),Max(ZRI12))
make grob solid "3dp_plot_name" ZRI12 x y 0.5 # scales for x,y and z

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