The human "magnesome": detecting magnesium [3751] binding sites on human proteins,

BMC Bioinformatics. 2012

“...Conclusion
In this work we address the problem of annotating magnesium binding sites in proteins starting from their sequence. We take advantage of an annotation resource recently introduced (BAR+, [13]), where functional and structural features derived from PDB structures are implemented into HMM models that allows sequence to template alignment even when sequence identity is below 30%. This procedure is based on the notion of "cluster", a set of sequences retrieved as connected components of a graph where two proteins are linked together when they share a sequence identity greater or equal than 40% in at least 90% of the pair wise alignment length. By restricting our analysis to clusters containing human sequences and magnesium binding PDB structures, we align with the cluster HMMs some 3,751 human sequences that fall in the same clusters and inherit by this the magnesium binding feature. Some 370 human sequences share an identity to the template less than 30%...”

full paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439678/