Does anybody have any idea about any online server that takes in multiple amino acid sequences in fasta format and outputs the 3D structure of the input amino acid sequences in the form of helix, sheet and coil? I searched but could not find any. There are servers that take in 1 sequence. I want to get the structure of multiple sequences together...
Unfortunately it is impossible to predict the tertiary structure of proteins using raw amino acid sequence. The information required to be computed in the construction of the dynamic protein shape is too large for any computer at the moment.
There are actually a list of research facilities that are looking for people to donate their computer's idle CPU time to help sequence proteins.
Here is a list: (http://www.hyper.net/dc-howto.html).
If you are only looking for secondary structure prediction you could try the JPred-server API.
On their website they refer to a script that
provides a JPred user with advanced functionality for an easy submission of hundreds of JPred jobs in a sustainable manner. […] For full details on the code, how-to, and for download please check Fabian's GitHub repository page.