Using core.find on a specific set of residues or domain

[Karan Kapoor]

Hello, I have aligned a set of PDBs of multi-domain transmembrane proteins using pdbaln and am now using core.find to search for the core residues. Is there a way to search for the core residues only in one of the domains (transmembrane domain in my case)? Currently the function finds the core in the intracellular domain that I am not interested in using for fitting the PDBs. Thanks for your time.

[Xinqiu Yao]

I don't think there is any argument to control where to find cores... One option is to truncate your 'pdbs' to contain only one domain, find the cores, and map core residues back to the full-length pdbs. Let me know if it works or if you have any further questions.

[Karan Kapoor]

Thanks. I will try out your suggestion.

[Barry Grant]

Perhaps a convenient approach might be to "mask" the portions of structure you do not want to feature in your core. For example, you could set the coordinates of your unwanted region to NA in the input to core.find() but then obviously use the unmasked coordinates fir further analysis.

Note to developers: Maybe we could have a mask= input option in there future or at the least a demonstration of how to do this in the Rd example section.

[Shahryar Alavi]

And a question about core.find() application.

It's been mentioned in the Principal Component Analysis Tutorial that using core.find() for structural superposition will highlight domain rearrangements. I have a trajectory of a multi-domain protein (with a hinge region) and I set its lmi() and cna() following both conventional and core.inds superpositions. The conventional method resulted in a DCCM with much more correlated residues and a CNA with more inter-domain communications.

In a similar research (http://dx.doi.org/10.1038/srep19940) I've read that we can assume whole of a multi-domain structure as a rigid body when its inter-residue generalised correlation (GC) coefficients are high (GC>0.2).

So, is there any "quantitative" criteria to assess when to use conventional or core.inds superposition?

Thanks.

[Karan Kapoor]

Thanks Barry, that may be easier to do.