A novel method for high accuracy sumoylation site prediction from protein sequences

Here we presented a statistical method for sumoylation site prediction. A 5-fold cross validation test over the experimentally identified sumoylation sites yielded excellent prediction performance with correlation coefficient, specificity, sensitivity and accuracy equal to 0.6364, 97.67%, 73.96% and 96.71% respectively. Additionally, the predictor performance is maintained when high level homologs are removed.By using a statistical method, we have developed a new SUMO site prediction method – SUMOpre, which has shown its great accuracy with correlation coefficient, specificity, sensitivity and accuracy.Sumoylation, a reversible post-translational modification (PTM) by the small ubiquitin-related modifier (SUMO) is essential to dozens of cellular activities, including subcellular transport, control of gross subnuclear architecture, direct and indirect effects on transcription, regulation of DNA damage recovery and replication, chromosome segregation, cell cycle progression, and competition with other ubiquitin-like modifiers (Ubls) [1-3]. Sumoylation is reportedly also a factor in various diseases and disorders, especially neural diseases, such as neuronal intranuclear inclusion disease (NIID), Alzheimer's disease (AD), and Parkinson's disease (PD) [4,5]. SUMO proteins are highly conserved across eukaryotes, and mammals express four highly conserved SUMO genes – SUMO-1, SUMO-2, SUMO-3, and SUMO-4-among which SUMO-1 has received the most attention. Yeasts express only a single SUMO gene, while plants express at least eight. However, the exact role played by such a modification – for example, positive or negative transcriptional regulation – is still unknown. Thus, more detailed information is needed on sumoylation substrates and sites.It was still widely accepted that ψKxE/D [6,7] (ψ represents a large hydrophobic amino acid and x represents any amino acid) is the consensus motif for SUMO-1 conjugation. However, there were many cases of sumoylation which did not occur