I know there is FOLDit and folding@home, but these only allow for working with structures provided by the authors.
Is there a program which I can load my own pdb file into and play around with the structure in three-dimensional space, playing around with possible secondary structures?
Yes. My protein of interest (solved structure) is supposed to perform a structural transition, and I want to try and model it using a computational approach. I would just need a program that calculates steric clashes, energies and so on, i order to check on the viability of the structure I model in 3D space.
You can try with PDBSUM (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html) or structure assignment of swiss model server (http://swissmodel.expasy.org/workspace/index.php?func=tools_structureassessment1).
And if you want to analyze in depth , you can use the score command of the Rosetta code. (https://www.rosettacommons.org/)
For a peptide you might play with Avogadro. If you consider larger proteins you might want to consider Dyana (Cyana). Although this is used for NMR, it allows you to do a few neat things. You need the sequence and you need to specify the phi/psi angles of the aa's. Then the prog will give you a bunch of structures that satisfy your constraints. If you now use distance restraints between the secondary structure elements you will begin to fold the protein. ... the more restraints the better (obviously). Even better if you have some experimental restraints.
This is however a text based program and it is not free. Suggest you find a local protein NMR guru to see if this is a viable approach for your problem...
i.e. see --> Biomolekulares Magnetresonanz Zentrum (BMRZ)
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