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
Hi,
The cleft analysis in PDBSum is done using SURFNET developed by Roman A Laskowski. You can refer to these papers for more details :
1) Laskowski, Roman A. "SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions." Journal of molecular graphics 13.5 (1995): 323-330.
2)Laskowski, Roman A., et al. "Protein clefts in molecular recognition and function." Protein science: a publication of the Protein Society 5.12 (1996): 2438.
or to the SURFNET manual available online from EBI : http://www.ebi.ac.uk/thornton-srv/software/SURFNET/ .
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