Constraints

Constraints

Site constraints:
Site constraints can either penalize or reward a residue for being at the interface, and decoys that fail to meet the constraint are rejected. A common use is when you are using a fragment of a multidomain protein for one docking partner. In this case, you might block the N and C termini of the fragment to reflect the fact that in reality, there is another part of the protein there.

A common case to use a rewarding site constraint is if experimental evidence has identified a given residue(s) as having a high probability of being at the interface. You can use a rewarding constraint to force that residue to be at the interface. My experience with rewarding constraints, however, is that they lead to a narrow diversity of predicted structures. A better strategy is to make a loose distance constraint between that residue and some other residue on the other docking partner.

Site constraint file format:
You can look at test.cst (a penalizing constraint) in the samplerun directory for an example. I display it here:

Pay close attention to this file format. Failure to provide ANY of the information above will result in an error.
To add more constraints, up the number of constraints (first line), and put in a new constraint as:

<penalty>
<residue 1>
...
<last residue>
<0 (chain of last constrained residue)>

Also, you will want to change the filter so that all constraints will be required.

For a rewarding constraint (not recommended), change the sign of both the penalty (now a bonus) and of the filter.

Distance constraints:
I have already discussed one case for using a distance constraint. Another case is if there is experimental evidence that residue x on partner A is within N Angstroms of residue y on partner B. You can put a constraint in that will require residues x and y to meet this distance.

Distance constraint file format:
This format is somewhat simpler than that of site constraints.

**************************
7.0                    #require the two residues to be within 7.0A of each other.
    370 A            ]the two residues.
    371 B            ]
**************************

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