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SitCon: binding site residue conservation visualization and protein sequence-to-function tool
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Orientador(es)
Resumo(s)
We introduce SitCon (SITe CONservation), a program designed to explore
conservation of functionally important sites in a series of hypothetically homologous
candidate protein structures, given amino acid sequence as an input. This can especially be
useful when looking for an unknown function of a protein. SitCon exploits the fact that
binding sites of proteins are preserved better than the overall residue sequence
conservation. To test the capability of unknown function prediction, we randomly chose
known function proteins from Caenorhabditis elegans genome. To imitate a behavior of an
unknown function target, only the low homology proteins with 0.01 E-score 100 were
analyzed as templates. Out of 29 enzyme targets, SitCon was able to provide various hints
about their function in at least 69% of the cases. For the eight nonenzyme targets, the
predictions matched in only 25% of the cases. SitCon was also tested for a capability to
predict presence or absence of metal-containing heterogroups in the target enzymes with
80% success rate. Because this algorithm is not based on specific protein signatures, it
may allow detection of overlooked relationships between proteins. SitCon is also very
effective as a tool allowing visual comparison of binding site residue conservation between
the target and homologous templates side-by-side.
Descrição
Palavras-chave
Genome Sequence-to-function Protein function prediction Binding site Amino acid residue conservation . Faculdade de Ciências Exatas e da Engenharia
Contexto Educativo
Citação
Kairys, V., & Fernandes, M. X. (2007). SitCon: Binding site residue conservation visualization and protein sequence‐to‐function tool. International Journal of Quantum Chemistry, 107(11), 2100-2110.
Editora
Wiley