Sorry if I seem to be fool. I am very new to Protein thing. What is the difference between 2D Protein Structure and Secondary Structure? If we say about 2D Structure, what are we talking about? Are we talking about alpha helix or beta sheets?
In case of Secondary structures, it's about alpha helix or beta sheets, more @ http://en.wikipedia.org/wiki/Protein_structure
In case of 2D structures, its just a method of representation (visualization) of protein structure, which is mainly aimed at inter-residue/strand contacts. More @ http://www.biostat.wisc.edu/bmi776/lectures/protein-structure.pdf
I have mentioned the links in above answer.. but as you are new to "protein thing".. I think you can try reading the wikipedia article carefully.. its very comprehensive and will be very helpful all around..
for 2d structure there is no such a documentation that I could find.. as its just a method to depict protein structure.. these are two examples where the protein is depicted in 2d structure:
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Do you have an example of such a usage? I've never heard of "2D structure" before, which is good since it wouldn't seem to make any sense.
Contact maps ring a bell here.. but indeed, 2D structure is weird.
That makes much more sense and seems to jive with the answer from rohan