I've never used this forum before, so please excuse any mistakes.
I'm trying to get some sorts of insights into the secondary structure and 3D folding of protein, which I'm trying to examine regarding its evolution insight archaea. Basically I'm pretty much done with the MSA and the building of the tree for the phylogenetics. But now I want to include some structural information in my research and I need a tool, which I can use to put in my alignment which I also used to build the tree and let it predict the secondary structure. I expect to see a highly conserved secondary structure and maybe some sort of little difference between maybe one or two groups.
Additionally it would be nice, if the same program could also predict the 3D folding of the proteins, create PDB's for each protein, superimpose them and calculate indiviual differences.
I know, that this is probably a giagantic mass of calculations and I actually don't expect a program to be accurate enough to be able to all these task.