1)I have some doubts on clustering. I have modeled a protein and refined its loop. How exactly clustering will help me in further steps? and whats going to be the output result which i can use later? and do i need to use relax_a_large_protein option to the final model? (my protein contains 290 amino acid) or directly use the final model for docking studies?
2) In protein-ligand docking protocols, unlike other softwares there is no protein preparation steps where we can minimize the total protein and add Hydrogen atoms. So is it fine to skip these steps and move further or should i use other softwares for this purpose?
Thank you in advance for all the suggestions.