If u could provide all sample input files of DOPE alignment that we input in R, then probably I could help u. Post the sample files (TvLDH.profile).

That's perfect!

1bdmA.profile and TvLDH.profile - these are the energetical profiles of both proteins

This is the alignment of those two proteins - the plot of profiles should be in accordance with this alignment

This is the final plot (note, that there are gaps in the curves - it due to gaps in alignment)

and this is the script in python - this script should run also in R, but it doesn't.

a little help:

#read data from profile files

prof1=read.table("1bdmA.profile", header=TRUE)

prof2=read.table("TvLDH.profile", header=TRUE)

# make 1 common table

allprofiles=cbind(prof1$"TOTAL", prof2$"TOTAL")

#plot profiles

matplot(dane, type="l", lty=1, lwd=2)

but this is without alignment.

#read the file, skip first 7 lines

data=read.table("1bdmA.profile",skip=7);

# Plot resid(column1) and total score(column 42), type of plot="l" (line plot)

plot(data$V1,data$V42,type="l",xlab="Resid",ylab="Total DOPE Score");

# Save the plot

savePlot("DopePlot.png");

As i have no idea how u want to plot, so i have plotted a basic line plot between resid and total dope score

I want to plot both curves (1bdmA.profile and TvLDH.profile) together in one plot (as an example DOPE_plot.jpg) in accordance to sequence alignment (TvLDH-1bdmA.ali) of both proteins.

OK, no problem. If you have no idea how to do it, I'll try in a free time and post it here.

Thanks ;)

Its seems simple to do. We need to first map both target and template residue wise and then map this alignment back to dope score. Same here ( ;) I too will do when get free time). Please post if u do :)

How do you generate the pharmacophore models of protein structures taking into consideration the active sites of these proteins... any free software??