Software Suggestions - Short Peptides - (Oct/01/2012 )

Hi, I am currently working with 14AA long peptides with a viral protease. I would like to examine the secondary structures of the peptides (14 amino acids in length). I need a software that I can put the sequence in and part of the output include: % alpha helix, % beta-sheet, % un-ordered. There has been precedence of this in the literature using 11AA peptides, but the software they cited, is no longer available (it was made in 1988). Please recommend software that is capable of this analysis. I recently used PEP-FOLD and I could not for the life of me find this analysis. If the software forms a 3D structure and includes all of the viewing tools, that is great, but I am really interested in looking at the secondary structure composition (% of each type) to report for the peptides I am using.

Thank You

Have you tried I-Tasser?

have you tried the expasy tools for protein structure?

mdfenko on Tue Oct 2 13:30:58 2012 said:

Thanks for this list, and I did look at I-TASSER after your post. I have determined values for what I was looking for but unfortunately for such short peptides they are not very insightful. I now would like to model these peptides into the protein of interest to help explain my findings. Unfortunately, I am in over my head with these programs (pyMol, autodock, to name a few) and I am looking for simple tutorials to get me started as I have no background in protein 3D modeling. Any links to literature, websites, tutorials, would be greatly appreciated.

Thanks