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Scans a protein and builds disulfides that join residues in one set of residues with those in another set. By default, non-protein, GLY, and PRO (or DPRO) residues are ignored. Residues to be joined must be min_loop residues apart in primary sequence. Potential disulfides are first identified by CB-CB distance, then by mutating the pair to CYS, forming a disulfide, and performing energy minimization. If the energy is less than the user-specified cutoff, it is compared with a set of rotations and translations for all known disulfides. If the "distance" resulting from this rotation and translation is less than the user-specified match_rt_limit, the pairing is considered a valid disulfide bond.
Once valid disulfides are found, they are combinatorially added. For example, if disulfides are identified between residues 3 and 16 and also between residues 23 and 50, the following configurations will be found: 1. [3,16] 2. [23,50] 3. [3,16],[23,50]
The mover is now able to place D-cysteine disulfides, beta-3-cysteine disulfides, and mixed D/L/beta-3 disulfides.
mutate_pro=trueoptions (see below).
<Disulfidize name="(&string)" scorefxn="(&string)" set1="(&selector)" set2="(&selector)" match_rt_limit="(&float 2.0)" score_or_matchrt="(&bool false)" max_disulf_score="(&float 1.5)" min_loop="(&int 8)" use_l_cys="(&bool true)" keep_current_disulfides="(&bool false)" include_current_disulfides="(&bool false)" use_d_cys="(&bool false)" use_beta_cys=(&bool false) mutate_gly="(&bool false)" mutate_pro="(&bool false)" />
EXAMPLE The following example looks for 1-3 disulfides. All found disulfide configurations are then designed using FastDesign.
<Disulfidize name="disulf" min_disulfides="1" max_disulfides="3" max_disulf_score="0.3" min_loop="6" /> <MultiplePoseMover name="multi_fastdes" > <ROSETTASCRIPTS> <MOVERS> <FastDesign name="fastdes" /> </MOVERS> <PROTOCOLS> <Add mover="fastdes" /> </PROTOCOLS> </ROSETTASCRIPTS> </MultiplePoseMover>
As of 29 September 2015, the Disulfidize mover works with symmetric poses, permitting disulfides to be built across symmetric interfaces. In this case, the min_disulfides and max_disulfides options represent the minimum and maximum number of unique disulfide pairs. Note that this is, at the current time, an experimental feature that may have bugs associated with it.