I ran ssdna-small ligand docking with haddock, which I increased the sampling size according to the guide and select all residues as active residues. All other parameters was kept default (but DNA restraint off since its ssdna). By running docking as described, I got confusing results as theres not clear dominant clusters, the results is very diverse, each cluster only have cluster size of <20. Is there any problem with the parameters that I can adjust to get better result? Im exploring the potential binding site as the ssdna is newly developed.
In blind docking it is not surprising to have very diverse results.
Did you increase the sampling?
Hi, yes I did increase the sampling size based on the guide to 10000/400/400. I understand having diverse results is normal for blind docking but I’m not sure how to analyze the result. Should I evaluate across all the results despite their cluster size, RMSD etc. but focus on searching for consistent interaction across all clusters or is there any specific metric I need to pay attention to? I’m not sure what to do next as the results are just too diverse, so it’s good if I can get some direction from here.