#13 improving the accuracy- optimizing the docking parameters

[sam]

Hi Segi,

I am testing the software on some known RNA-ligands cases, but the RMSD's are not promising. I am getting different ranges from 2.4 to 15! I played with the receptor flexibility from 0 to 3 and the radius around the reference ligands and the receptor from 6 to 15. however the results didn't get improved. I was wondering if you have any recommendations for me to get a better results? Since in our cases we don't know the receptor and the binding sites, we need to screen everywhere basically. Please help me with that so I can still use the rdock.

Best,
Sam