Your question is very strange. Bioinformatics tools are not used aseptically and without an end. Which properties of your proteins do you intend to highlight, and to show what? Do you want to study their evolution or want to study their structure? Generally, bioinformatics tools are used to direct the experimental work (reducing time and avoiding unnecessarily spending money), or to complement and / or explain experimental data already possessed. What do you really want to do?
if you are not clear, I can't help you. When do you say proteins (plural) of what are you talking about? Of globular proteins or intrinsically disordered proteins? Are proteins belonging to the same family or are different proteins?
If you want, you can send an email to [email protected] with more details and I will try to suggest something to you.