There are methods currently used to characterize protein structure and function ...Most nuclear proteins for example contain one or more specific short sequences of amino acids that serve as .........YOU can refer to Molecular biology of the cell 4th. edition , and on the section " Analyzing Protein Structure and Function"ncbi.nlm.nih.gov
If you would like to mutate one of the residues of the peptide Pymol software handles it. Avogadro software is useful to create various sequences of peptides. Modification of the ligand is also doable by means of Avogadro.