Any of you have a favorite program – freely available on the web and easy to use- for prediction of protein secondary structure… and comparison to known secondary structures…??
One of the things that I do for a living, and for fun frankly, is to identify and characterize genes that my favorite organism (MFO) can’t live without in vivo, but can do without in vitro. A rather large proportion of the set of genes that I care about are ‘hypothetical’ and many of them have no homology what-so-ever in primary sequence at the protein level to things in publicly available databases. As a result of this, the downstream work of characterizing what these genes (that we have already demonstrated are very important for the biology of the organism during disease) actually do involves quite a bit of detective work and can be very challenging. I love this aspect of my projects- because I love pulling the thread and unraveling the story. These projects force us to use a very broad range of biological tools, bioinformatics etc- and I am sure in the future we are going to have to become better biochemists.
Anyway- right now… right this minute- … I need you structural people to cough up your recommendations for secondary structural prediction … for proteins…
Thanks in advance!