I'm new to the field but doing a project on predicting tertiary or secondary structure of peptide fragments. Basically, a few papers have been looking at the effects of small fragments of the parent peptide hormone (leptin), and I'm interested in modelling the predicted structure of those fragments. Some fragments are as few as 9 residues but can still activate the receptor while other fragments that are similar in length and sequence will do just the opposite. So perhaps these fragments are doing funky things when separated from the main protein. So what kind of server would be good to model these? I don't know if I should stick with threading servers or incorporate ab initio modelling, or what. Furthermore, I would love for someone to recommend a good server that is generally reliable (i.e. I can't wait 6 months to get my request processed!). There are too many out there.
Lastly, if anyone knows any good servers/programs that can make pretty sequence alignments, say for a poster or powerpoint, I would really appreciate it.