docking.py auto-detect partners

[Anonymous]

how can i run docking script when i dont know the partners?? pdb file generated from protein modeller contain no such information about side-chains…
is there a way to set default value for partners which run on all models by auto-detecting partners??

[Anonymous]

I’m not quite sure I understand the question (s). First – Are you trying to find what docking partners your protein has from your list of possible candidates that have known structure? What do you mean by protein modeller? Rosetta? from the docking.py script?

[Anonymous]

InterfaceAnalyzer will generate a list of residues that are at the interface (and handy PyMOL selections). It is not guarunteed to be the same residues that docking considers to be at the interface, however.

[Anonymous]

thanx all that problem is solved now actually i was using modeller from salilab.org and then pyrosetta for docking…..now plz help me out in this issue “how can i dock protein with single partner (sidechain) by pyrosetta?? e.g we use A_B for 2 chains but what can i do if i have only chain A??

[Anonymous]

i have protein with chain A only and 3 ligands….got me? if yes then kindly tell what should i mention in partners?

[Anonymous]

You can’t dock a protein that only has one chain without having something else to dock it to. I don’t understand your question.

[Anonymous]

Understood! What you need to be doing is ligand docking, not protein-protein docking. If you are using the http://graylab.jhu.edu/pyrosetta/downloads/scripts/demos/D120_Ligand_interface.py script, I think it only supports docking one ligand at a time, in which case you’d use whatever chain letter that one ligand has in the PDB file for your partners flag.

[Anonymous]

hmm alright so you mean i can’t dock all 3 ligands at a time….and one more thing plz can i join all three docking scripts (protein,ligand,dna) in one script? because i am developing a tool and its rubish to say user to click here for protein or click here for ligand docking….what you say?

[Anonymous]

You absolutely _can_ do any sort of docking you could imagine with a PyRosetta script – it’s just that the provided sample script probably only allows for docking one ligand at a time. If you are writing your own script there’s no reason not to aim for docking multiple things at a time, it just has to be written differently.

If you wanted one script that did protein-protein docking, protein-ligand docking, and protein-DNA docking…it could be presented as one script at the command-line level, but there would be a LOT of unshared code that was different between the three modes. In particular they would use different scorefunctions and probably different code to set up the FoldTree for docking. You might or might not be able to get away with reusing the Monte Carlo algorithm that actually moves the molecules and tests new conformations.

[Anonymous]

Multiple ligand docking can be performed with the XML/RosettaScripts interface. See Lemmon & Meiler, “Rosetta Ligand docking with flexible XML protocols” Methods Mol Biol. 2012;819:143-55. http://www.meilerlab.org/index.php/publications/showPublication/pub_id/119

Regarding one tool for all sorts of docking, one way to make the tool is to autodetect if the binding partner is more protein-like, small-molecule-like or DNA-like and then automatically start protocol one, two or three based on it.

While both the ligand docking and protein-protein docking protocols are rather similar, and one might theoretically make a common protocol which could handle both, it’s the small differences which will get you. While a single standard scorefunction is somewhat of a goal, ligand docking and protein-protein docking use different scoring. Some of that is technical (e.g. protein-protein docking uses a statistical residue pair potential but ligand docking needs to add in Coulombic electrostatics because we don’t have statistics for the ligand) and some of that is just that you get better results with one scorefunction in ligand docking and a different one for protein-protein docking. The search algorithm is slightly different as well – there’s many fewer degrees of freedom in ligand docking versus protein-protein docking, so different search techniques are used. Most notably, centroid mode is used in protein-protein docking to find the starting configurations, but ligand docking can avoid centroid mode issues and operate solely in full-atom mode. — It’s unlikely a single combined protocol would work as well as separate, specialized protocols.

[Anonymous]

yeah! got it…nice explanation i think autodetection is the best option.

[Author]

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