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Open Access Research article

An approach to large scale identification of non-obvious structural similarities between proteins

Artem Cherkasov1* and Steven JM Jones2

Author Affiliations

1 Division of Infectious Diseases, Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada

2 Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada

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BMC Bioinformatics 2004, 5:61  doi:10.1186/1471-2105-5-61

Published: 17 May 2004



A new sequence independent bioinformatics approach allowing genome-wide search for proteins with similar three dimensional structures has been developed. By utilizing the numerical output of the sequence threading it establishes putative non-obvious structural similarities between proteins. When applied to the testing set of proteins with known three dimensional structures the developed approach was able to recognize structurally similar proteins with high accuracy.


The method has been developed to identify pathogenic proteins with low sequence identity and high structural similarity to host analogues. Such protein structure relationships would be hypothesized to arise through convergent evolution or through ancient horizontal gene transfer events, now undetectable using current sequence alignment techniques. The pathogen proteins, which could mimic or interfere with host activities, would represent candidate virulence factors.

The developed approach utilizes the numerical outputs from the sequence-structure threading. It identifies the potential structural similarity between a pair of proteins by correlating the threading scores of the corresponding two primary sequences against the library of the standard folds. This approach allowed up to 64% sensitivity and 99.9% specificity in distinguishing protein pairs with high structural similarity.


Preliminary results obtained by comparison of the genomes of Homo sapiens and several strains of Chlamydia trachomatis have demonstrated the potential usefulness of the method in the identification of bacterial proteins with known or potential roles in virulence.