Dataset Information
SODa: an Mn/Fe superoxide dismutase prediction and design server.
Ontology highlight
ABSTRACT: Background
Superoxide dismutases (SODs) are ubiquitous metalloenzymes that play an important role in the defense of aerobic organisms against oxidative stress, by converting reactive oxygen species into nontoxic molecules. We focus here on the SOD family that uses Fe or Mn as cofactor.Results
The SODa webtool http://babylone.ulb.ac.be/soda predicts if a target sequence corresponds to an Fe/Mn SOD. If so, it predicts the metal ion specificity (Fe, Mn or cambialistic) and the oligomerization mode (dimer or tetramer) of the target. In addition, SODa proposes a list of residue substitutions likely to improve the predicted preferences for the metal cofactor and oligomerization mode. The method is based on residue fingerprints, consisting of residues conserved in SOD sequences or typical of SOD subgroups, and of interaction fingerprints, containing residue pairs that are in contact in SOD structures.Conclusion
SODa is shown to outperform and to be more discriminative than traditional techniques based on pairwise sequence alignments. Moreover, the fact that it proposes selected mutations makes it a valuable tool for rational protein design.
SUBMITTER: Kwasigroch JM
PROVIDER: S-EPMC2442099 | biostudies-literature | 2008 Jun
REPOSITORIES: biostudies-literature
Publications
SODa: an Mn/Fe superoxide dismutase prediction and design server.
BMC bioinformatics 20080602
<h4>Background</h4>Superoxide dismutases (SODs) are ubiquitous metalloenzymes that play an important role in the defense of aerobic organisms against oxidative stress, by converting reactive oxygen species into nontoxic molecules. We focus here on the SOD family that uses Fe or Mn as cofactor.<h4>Results</h4>The SODa webtool http://babylone.ulb.ac.be/soda predicts if a target sequence corresponds to an Fe/Mn SOD. If so, it predicts the metal ion specificity (Fe, Mn or cambialistic) and the oligo ...[more]