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!
Blue Lab Coats 
how about sending us structural biologists the gene sequence of interest — that way we can solve the structure!
There’s a whole slew of secondary structure prediction programs at expasy.org (and many other useful tools). I’m partial to PredictProtein, but generally recommend using a bunch and going with the consensus.
Enrique- Are you volunteering to have a go?
Odyssey- I have tried PredictProtein- do you use only the basic version- or do you subscribe to the additional stuff? I recall that there is also threading program that I used to use, for which the name now escapes me (it’s been a while!)…Hell if I know what I did with the bookmark… I was hoping that one of you would have it on the tip of your tongue!!
You also might want to try a fold prediction server or Robetta
I’ll take a stab at a suggestion – have you tried Geneious (available at http://www.geneious.com/)?
You enter a sequence and it gives you the protein structure which you can manipulate any which way you want… watch the demo
http://www.geneious.com/assets/demonstrations/GeneiousPro4.5.html
I used a trial version of Geneious for a bit, but there were too many bells and whistles and not enough time for me to learn to play a tune.
Good luck.
There’s a whole bunch of things here: http://www.cbs.dtu.dk/services/
I’ve only used a couple of things (and not for protein structure), but they were really intuitive.
I just use the basic version of PredictProtein. And I take all predictions with a very large pinch of salt – I used to work in that broad area.
Was the threading program SwissModel? You can get to that through expasy.org as well (and other threading/homology programs). I also just use the basic/standard settings for that. However, it won’t be much help if your sequence has no homology to a known structure…
Rosetta (also available through expasy.org) is quite good for ab initio predictions. Or at least as good as the current state of the art allows…
Hey- Thanks for all the excellent suggestions- I’m going to have some time this evening in my office without meetings and other assorted nonsense to deal with- and I’m going to test them all out!
Odyssey- I don’t think it was SwissModel- It had a weird name that I is just beyond the reach of my memory… which is making me crazy!!
I’ve used PsiPred and PONDR before…
Just Another PhD,
PONDR is a good idea. It doesn’t predict structure – it predicts a lack of structure. In other words, disorder. It’s actually more accurate than most secondary structure predictors.
My grad student found the server for fold prediction I was thinking of- it is 3D-PSSM, just in case any of you has any need. But- the better version is phyre…and it can be found here.
I’ve tried most of them. I suggest JPRED, from Scotland.