ArticleBMC bioinformatics2008
SODa: an Mn/Fe superoxide dismutase prediction and design server.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin.Protein science : a publication of the Protein Society · 2022Article
- Interchangeable utilization of metals: New perspectives on the impacts of metal ions employed in ancient and extant biomolecules.The Journal of biological chemistry · 2021Review
- Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface.Environmental microbiology · 2019Article
- Article
- Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Homology modeling and comparative profiling of superoxide dismutase among extremophiles: exiguobacterium as a model organism.Indian journal of microbiology · 2014Article
- Biochemical characterization of psychrophilic Mn-superoxide dismutase from newly isolated Exiguobacterium sp. OS-77.Extremophiles : life under extreme conditions · 2014Article
- Detection and characterisation of mutations responsible for allele-specific protein thermostabilities at the Mn-superoxide dismutase gene in the deep-sea hydrothermal vent polychaete Alvinella pompejana.Journal of molecular evolution · 2013Article
- Molecular cloning, purification, and characterization of a superoxide dismutase from a fast-growing Mycobacterium sp. Strain JC1 DSM 3803.Journal of microbiology (Seoul, Korea) · 2011Article
- Buffer optimization of thermal melt assays of Plasmodium proteins for detection of small-molecule ligands.Journal of biomolecular screening · 2009Article
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4 authors.
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Abstract
backgroundSuperoxide 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.
resultsThe 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.
conclusionSODa 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.
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