Hi, I'm a beginner in the field of bioinformatics. I need to model peptides (+-16a.a.) obtained from the in silico hydrolysis of a protein. I'm not sure which technique and software would be most suitable. I don't understand in this case if I should use techniques by ab initio, threading or homology modeling. Pepfold, deepfold, I-TASSER or others? Could anyone help?
Thank you for your attention! Peptides are obtained from hydrolysis with enzymes from the gastrointestinal tract. Previous supplementation with this natural whole protein has shown anti-obesity activity in an animal model. The objective would be to model these peptides resulting from the hydrolysis of this protein by digestive enzymes (peptides that have around 12-18 amino acids). The aim is to further correlate the activity of these peptides after digestion with the activity displayed in vivo by performing docking/dynamics with a therapeutic target of obesity (in physiological conditions). Could you understand better?