Hi Rosetta Users,
I have a couple of questions on score functions that appeared in the protein-ligand tutorial. In the docking protocol XML file ( https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/docking/dock.xml ), the score functions used are ‘ligand_soft_rep’ and ‘hard_rep’ with their corresponding weights for ‘HighResDocker’ and ‘FinalMinimizer’ movers. In the options list ( https://www.rosettacommons.org/demos/latest/tutorials/ligand_docking/answers/docking/options ), there is a flag state ‘-restore_pre_talaris_2013_behavior true’ which restores some parameters to earlier values.
So, my questions/confusions are:
- Is my understanding correct that weights are given in the XML file, and a specific score function is given in the options list?
- What score function actually used in this tutorial? How did the flag ‘restore_pre_talaris_2013_behavior’ change the behavior on score functions: ‘ligand_soft_rep’ and ‘hard_rep’ in this case?
- How can I appropriately implement other score functions? For example, if I want to use ref2015 or betanov16, do I need to change the weight in the XML? And what do I need to do for the options list?
- Does the mover sequence in <movers>…</movers> and <protocols>…</protocols> matter? If it does, for example, when I add a new mover that adds water molecules to the interface, is it right to place it after ‘transform’ and before ‘high_res_docker’ mover?
I also tried to use GALigandDock mover, but it failed. What I know about GALigandDock is that it takes a ligand-protein complex as input and optimizes ligand conformation to predict docked structure. I attached the files I used for GALigandDock, and I appreciate any feedback. Since GALigandDock analyzes ligand structure, is it possible to add it after 'final_minimizer' and before 'InterfaceScoreCalculator' to better predict the docked structure? Or maybe just after 'High_res_dock'?
I appreciate any help! And shout out to this forum, I've learned so much from you all!
This is the XML for GALigandDock I used:
<ScoreFunction name="dockscore" weights="beta_genpot">
<Reweight scoretype="fa_rep" weight="0.2"/>
<Reweight scoretype="coordinate_constraint" weight="0.1"/>
<ScoreFunction name="relaxscore" weights="beta_genpot_cart"/>
<GALigandDock name="dock" runmode="dockrigid" scorefxn="dockscore" scorefxn_relax="relaxscore" nativepdb="6WNP_crystal.pdb"/>