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

Background: 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. Results: 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 ...

• Type: Journal
• Year: 2004
• Where: BMCBI
• Authors: Artem Cherkasov, Steven J. M. Jones
• Keywords: BMCBI 2004, Horizontal Gene Transfer, Proteins, Structural Similarity