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Reference: Cheng T.M.K., Lu Y-E, Vendruscolo M., Lio P., Blundell T.L. Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms. PLoS Comp. Biology.(2008) 4 (7) e1000135.
Hosted: Hosted by Cambridge University – THIS TOOL IS NOT CURRENTLY WORKING (http://www.bongo.cl.cam.ac.uk/Bongo2/Bongo.html)

Summary:
BONGO makes predictions of variant disease susceptibility based on the changes they cause to the protein structure. It uses graph theoretical measures to captures differences in amino acid interaction networks.

Methodology:
• A protein structure is converted to a graph, based on its amino acid interactions. Those residues of key importance for structural stability are determined by these interactions.
• The substituted amino acids are modelled and the impact of the change determined based on the changes in the network.
• Differences in key amino acids are more likely to be associated with disease.
• It has been calibrated using p53 and the known structural consequences of core mutations.

Input:
A protein structure is required. This can be entered by PDB ID or pasted into the submission form. The original and substituted amino acids are required along with the residue number (corresponding to the PDB file numbers).