I have a data set of peptides containing their sequences. I need to define their configuration (being linear or cyclic) and I don’t know its terms. are there any software or packages on R studio so i could use them, or should I define them one by one?
Yes, Download YASARA then download the package for Amino Acids or the full package, this will allow you to actually molecular model the peptide chains and see the exact shape of the protein structure generated but warning you will need a computer with a Fast Processor, Powerful Graphics Card, and much R.A.M. this program is very resource intensive. This program will also do a molecular simulation for protein folding if you run the Brownian Motion Simulation. http://www.yasara.org