I have done analysis of my protein's predicted 3D structure in PDBSum. I almost understood all analysis except the cleft analysis. Anybody have any idea, or reference on how this analysis is discussed? I could explain clefts with the amino acids they have, but is it the only interpretation of that or am I missing something?

PDBSum: http://www.ebi.ac.uk/pdbsum/

An example pdb cleft analysis: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=1ifq&template=clefts.html&r=speedfill

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