I am using Haddock to compare docking simulations of mutants of a protein with peptides.
I am using the same AIRs (NMR derived binding residues for each docking job). Although I have found run to run I get slightly variable results. In that haddock scores and cluster, sizes, etc differ.Even if I submit the same files with the same options (with random AIR exclusion turned on as a default). Just trying to understand what I am doing wrong or could change to remedy this?
I have been considering if the Random AIRs are actually hindering me in my particular use I know I can turn them off but I first wanted to understand if I am understanding correctly how they work. Each time I submit a job I specify a list of say 10 AIRs the random exclusion default means 50% are excluded so AIR 1,5,7,9,10 in 1 submission but in the next it could be 2,5,7,8, and 9. Or do the random exclusions vary within each job?