Hello,

I have been working on algorithms that extract co evolutionary signatures from protein sequence. As a result of my work I got some evolutionary information which possibly explains cotranslational protein folding. Most of the proteins under analysis were following the co evolutionary signature which I got but a small set of them are not. Now I'm very curious to attack on those proteins, which are deviating.

For this I need various intra protein structural parameters and sequence related parameters to compare proteins. RMSD is something that compares two protein structures for their similarity. But I don't want to compare them in this way. I need a complete set of structural (intra protein) parameters as well as sequence parameters (like residue conservation in a sequence) with which I can compare two proteins after normalizing to their lengths (sizes). I just need hints like hydropathic value of a protein, residue conservation in a sequence..etc.