Sherif Elsabbagh

thanks so much.. because I always use open babel to generate 3D conformer with --minimize .. but someone mentioned that you do not need this. just convert to 3D..

I know this might be a very basic question. But I need to make sure. Before using smina, is it really necessary to minimize ligands ? Because I read somewhere else a comment saying that ligand energy minimization is not that necessary

perfect i will try it thanks so much

perfect i will try it thanks so much

sorry i didnt know that.. so you mean to apply other docking softwares and use consensus docking scores.. but nothing can be changed within smina itself..

Hi I have a question. I tried to validate the docking experiment by first running docking of actives and decoys against the target protein. I drawed the ROC and the AUC was calculated as 0,65.. In this case, what can be done to improve this score. How can i manipulate the software to enhance the score thanks

Hi again.. I managed to find another tool called sdsort but when i use it I have a txt file like this REC minimizedAffinity 001 -10.807 0.000 002 -10.192 0.000 003 -10.044 0.000 004 -10.043 0.000 005 -9.874 0.000 006 -9.844 0.000 007 -9.796 0.000 008 -9.742 0.000 009 -9.698 0.000 010 -9.671 0.000 011 -9.567 0.000 012 -9.490 0.000 013 -9.449 0.000 014 -9.430 0.000 015 -9.407 0.000 016 -9.392 0.000 017 -9.280 0.000 018 -9.102 0.000 019 -9.098 0.000 020 C -9.088 0.000 021 C077 -9.066 0.000 022 -9.064...

sorry for all these questions but I cant find any other alternative to this tool