Icouldnot find DDMI protocol for design protein

[Anonymous]

Hello

I want to design my protein by Rossetta according to DDMI protocol that is used in article”computational design of PAK1 binding protein”.In this article designing of protein PAK1 done by protocol DDMI in Rossetta version 2.1. but i could not find this protocol in Rossetta 3.0. Do this protocol exist in Rossetta 3.0 with different name or this protocol removed in Rossetta3.0?the command line of this protocol according to the article mentions below:

rosetta.gcc –design –dock_des_min_inter –s input.pdb –linmem_ig –ex1 –ex2 –exOH

– extrachi_cutoff 1 –no_his_his_pairE –series qq –protein input –chain _ –

read_all_chains – multi_chain –randomize2 –resfile input.resfile –

multi_cool_annealer –try_both_his_tautomers – set_interface_cutoff 7.0 –nstruct 100

–ddmi_dUns_filter 4 –ddmi_dG_dSASA_ratio_filter_0.013

rosetta.gcc –design –design_min_inter –series qq –protein input –s input.pdb –chain

_ -resfile input.resfile –no_his_his_pairE –read_all_chains –multi_chain –

design_trials –extrachi_cutoff 1 –ex1 –ex2aro_only

thanks

[Anonymous]

As far as I’m aware, that protocol isn’t availible in Rosetta3 as a pre-fab program per se. Much of the dock/design protocols have transitioned to RosettaScripts, which allow you to put together such multi-stage protocols in a flexible manner.  I might suggest looking for more recent papers that do docking and design to see how they’re doing it.

Alternatively, you can take a look a the protein docking and protein design tutorials, which are availible as separate steps. Specifically, I’d recommend the Rosetta/demos/tutorials/advanced_protein-protein_docking/ and the Rosetta/demos/tutorials/protein_design/ tutorials, both of which are RosettaScripts based. (Alternatively, you can look at the Meiler Lab tutorials for docking and design at http://meilerlab.org/index.php/rosetta-tutorials). It should be relatively straightforward to make a combined dock/design protocol by combining the XMLs of each in the appropriate fashion.

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