In a previous post, I tried to explain what are proteins blocks (PBs). For those who forgot, PBs are structural prototypes used to modelize a 3D local protein structure into a 1D sequence. I illustrated this with a picture of protein blocks that I also posted on Flickr.

I initially …

I am now on sabbatical in Pointe-Noire, Congo for a while. My research activity might be slowed. Nonetheless, I count on you to increase my h-index by citing my papers has much as you can ;-)

Picture from Flickr. Creative Commons CC-BY.

I found this awesome tee-shirt in the Bytesize Bio …

Note to self.
Add the following lines to .bashrc file to clean Gromacs backups :

# clean Gromacs backups in the current directory
alias cleangromacsbackups="rm -f \#*\#"
# clean Gromacs backups recursively (for the fearless warriors)
alias cleangromacsbackups_rec="find ./ -name \#*\# | xargs -r rm"

Be careful with the second command...

Here is a simple pdb to fasta format conversion tool. The purpose was to extract residue sequence from atomic coordinates (ATOM lines).

Note that the sequence extracted this way corresponds to residues which are really present in the 3D structure. This could be different from the sequence obtained from the …