{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T12:50:22Z","timestamp":1762865422578},"reference-count":27,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The SODa webtool<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/babylone.ulb.ac.be\/soda\" ext-link-type=\"uri\">http:\/\/babylone.ulb.ac.be\/soda<\/jats:ext-link>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>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.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-9-257","type":"journal-article","created":{"date-parts":[[2008,6,3]],"date-time":"2008-06-03T06:13:33Z","timestamp":1212473613000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["SODa: An Mn\/Fe superoxide dismutase prediction and design server"],"prefix":"10.1186","volume":"9","author":[{"given":"Jean Marc","family":"Kwasigroch","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ren\u00e9","family":"Wintjens","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dimitri","family":"Gilis","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marianne","family":"Rooman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,6,2]]},"reference":[{"key":"2242_CR1","first-page":"598","volume":"119","author":"B Halliwell","year":"1992","unstructured":"Halliwell B, Gutteridge J, Cross C: Free radicals, antioxidants and human disease. Where are we now? J Lab Clin Med 1992, 119: 598\u2013662.","journal-title":"J Lab Clin Med"},{"key":"2242_CR2","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1016\/j.jbspin.2007.02.002","volume":"74","author":"V Afonsoa","year":"2007","unstructured":"Afonsoa V, Champya R, Mitrovica D, Collina P, Lomri A: Reactive oxygen species and superoxide dismutases: Role in joint diseases. Joint Bone Spine 2007, 74: 324\u2013329. 10.1016\/j.jbspin.2007.02.002","journal-title":"Joint Bone Spine"},{"key":"2242_CR3","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1038\/sj.gt.3303004","volume":"15","author":"J Greenberger","year":"2008","unstructured":"Greenberger J: Gene therapy approaches for stem cell protection. Gene Therapy 2008, 15: 100\u2013108. 10.1038\/sj.gt.3303004","journal-title":"Gene Therapy"},{"key":"2242_CR4","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1179\/135100003225002871","volume":"8","author":"D Dive","year":"2003","unstructured":"Dive D, Gratepanche S, Yera H, B\u00e9cuwe P, Daher W, Delplace P, Odberg-Ferragut C, Capron M, Khalife J: Superoxide dismutase in Plasmodium : a current survey. Redox Report 2003, 8: 265\u2013267. 10.1179\/135100003225002871","journal-title":"Redox Report"},{"issue":"Pt 6","key":"2242_CR5","doi-asserted-by":"publisher","first-page":"1318","DOI":"10.1042\/bst0311318","volume":"31","author":"J Whittaker","year":"2003","unstructured":"Whittaker J: The irony of manganese superoxide dismutase. Biochem Soc Trans 2003, 31(Pt 6):1318\u20131321.","journal-title":"Biochem Soc Trans"},{"key":"2242_CR6","doi-asserted-by":"crossref","first-page":"10695","DOI":"10.1016\/S0021-9258(18)90567-3","volume":"259","author":"W Stallings","year":"1984","unstructured":"Stallings W, Pattridge K, Strong R, Ludwig M: Manganese and iron superoxide dismutases are structural homologs. Journal of Biological Chemistry 1984, 259: 10695\u201310699.","journal-title":"Journal of Biological Chemistry"},{"key":"2242_CR7","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1093\/protein\/1.5.393","volume":"1","author":"M Parker","year":"1987","unstructured":"Parker M, Blake C, Barra D, Bossa F, Schinina M, Bannister W, Bannister J: Structural identity between the iron-and manganese-containing superoxide dismutases. Protein Engineering 1987, 1: 393\u2013397. 10.1093\/protein\/1.5.393","journal-title":"Protein Engineering"},{"key":"2242_CR8","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1016\/0014-5793(88)81160-8","volume":"229","author":"M Parker","year":"1988","unstructured":"Parker M, Blake C: Iron- and manganese-containing superoxide dismutases can be distinguished by analysis of their primary structures. FEBS Letters 1988, 229: 377\u2013382. 10.1016\/0014-5793(88)81160-8","journal-title":"FEBS Letters"},{"key":"2242_CR9","unstructured":"HTML to PDF conversion[http:\/\/www.rustyparts.com\/pdf.php]"},{"key":"2242_CR10","doi-asserted-by":"publisher","first-page":"9248","DOI":"10.1074\/jbc.M312329200","volume":"279","author":"R Wintjens","year":"2004","unstructured":"Wintjens R, No\u00ebl C, May A, Gerbod D, Dufernez F, Capron M, Viscogliosi E, Rooman M: Specific and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons. Journal of Biological Chemistry 2004, 279: 9248\u20139254. 10.1074\/jbc.M312329200","journal-title":"Journal of Biological Chemistry"},{"key":"2242_CR11","doi-asserted-by":"publisher","first-page":"1564","DOI":"10.1002\/prot.21650","volume":"70","author":"R Wintjens","year":"2008","unstructured":"Wintjens R, Gilis D, Rooman M: Mn\/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence. Proteins 2008, 70: 1564\u20131577. 10.1002\/prot.21650","journal-title":"Proteins"},{"key":"2242_CR12","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1093\/nar\/gkg095","volume":"31","author":"B Boeckmann","year":"2003","unstructured":"Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M: The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31: 365\u2013370. [http:\/\/www.expasy.org\/sprot] 10.1093\/nar\/gkg095","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"2242_CR13","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1016\/S0968-0004(98)01253-5","volume":"23","author":"K Henrick","year":"1998","unstructured":"Henrick K, Thornton JM: PQS: a protein quaternary structure file server. Trends Biochem Sci 1998, 23(9):358\u201361. [http:\/\/pqs.ebi.ac.uk\/] 10.1016\/S0968-0004(98)01253-5","journal-title":"Trends Biochem Sci"},{"key":"2242_CR14","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1093\/protein\/8.7.647","volume":"8","author":"N Boutonnet","year":"1995","unstructured":"Boutonnet N, Rooman M, Ochagavia M, Richelle J, Wodak S: Optimal protein structure alignments by multiple linkage clustering: application to distantly related proteins. Protein Engineering 1995, 8: 647\u2013662.","journal-title":"Protein Engineering"},{"key":"2242_CR15","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/nar\/28.1.235","volume":"28","author":"H Berman","year":"2000","unstructured":"Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, Weissig H, Shindyalov I, Bourne P: The Protein Data Bank. Nucleic Acids Research 2000, 28: 235\u2013242. 10.1093\/nar\/28.1.235","journal-title":"Nucleic Acids Research"},{"key":"2242_CR16","doi-asserted-by":"publisher","first-page":"1646","DOI":"10.1021\/bi00005a021","volume":"34","author":"M Lah","year":"1995","unstructured":"Lah M, Dixon M, Pattridge K, Stallings W, Fee J, Ludwig M: Structure-function in Escherichia coli iron superoxide dismutase: comparisons with the manganese enzyme from Thermus thermophilus . Biochemistry 1995, 34: 1646\u20131660. 10.1021\/bi00005a021","journal-title":"Biochemistry"},{"key":"2242_CR17","doi-asserted-by":"publisher","first-page":"4876","DOI":"10.1093\/nar\/25.24.4876","volume":"25","author":"JD Thompson","year":"1997","unstructured":"Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25: 4876\u20134882. 10.1093\/nar\/25.24.4876","journal-title":"Nucleic Acids Res"},{"key":"2242_CR18","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1093\/bioinformatics\/14.9.755","volume":"14","author":"S Eddy","year":"1998","unstructured":"Eddy S: Profile Hidden Markov Models. Bioinformatics 1998, 14: 755\u2013763. 10.1093\/bioinformatics\/14.9.755","journal-title":"Bioinformatics"},{"key":"2242_CR19","doi-asserted-by":"publisher","first-page":"276","DOI":"10.1016\/S0168-9525(00)02024-2","volume":"16","author":"P Rice","year":"2000","unstructured":"Rice P, Longden I, Bleasby A: EMBOSS: the European Molecular Biology Open Software Suite. Trends in Genetics 2000, 16: 276\u2013277. [http:\/\/emboss.sourceforge.net] 10.1016\/S0168-9525(00)02024-2","journal-title":"Trends in Genetics"},{"key":"2242_CR20","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.1006\/jmbi.1994.0105","volume":"246","author":"J Cooper","year":"1995","unstructured":"Cooper J, McIntyre K, Badasso M, Wood S, Zhang Y, Garbe T, Young D: X-ray structure analysis of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis at 2.0 Angstroms resolution reveals novel dimer-dimer interactions. Journal of Molecular Biology 1995, 246: 1531\u2013544. 10.1006\/jmbi.1994.0105","journal-title":"Journal of Molecular Biology"},{"key":"2242_CR21","unstructured":"PyMol[http:\/\/pymol.sourceforge.net]"},{"key":"2242_CR22","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.gene.2006.08.020","volume":"387","author":"B Dash","year":"2007","unstructured":"Dash B, Metz R, Huebner H, Porter W, Phillips T: Molecular characterization of two superoxide dismutases from Hydra vulgaris. Gene 2007, 387: 93\u2013108. 10.1016\/j.gene.2006.08.020","journal-title":"Gene"},{"key":"2242_CR23","doi-asserted-by":"publisher","first-page":"1377","DOI":"10.1016\/j.biochi.2006.04.005","volume":"88","author":"I Castellano","year":"2006","unstructured":"Castellano I, A DM, Ruocco M, Chambery A, Parente A, Di Martino M, Parlato G, Masullo M, De Vendittis E: Psychrophilic superoxide dismutase from Pseudoalteromonas haloplanktis : biochemical characterization and identification of a highly reactive cysteine residue. Biochimie 2006, 88: 1377\u20131389. 10.1016\/j.biochi.2006.04.005","journal-title":"Biochimie"},{"key":"2242_CR24","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1134\/S000629790601010X","volume":"71","author":"M Davydova","year":"2006","unstructured":"Davydova M, Gorshkov O, Tarasova N: Periplasmic superoxide dismutase from Desulfovibrio desulfuricans 1388 is an iron protein. Biochemistry (Mosc) 2006, 71: 68\u201372. 10.1134\/S000629790601010X","journal-title":"Biochemistry (Mosc)"},{"key":"2242_CR25","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1016\/S1016-8478(23)10728-X","volume":"23","author":"S Seo","year":"2007","unstructured":"Seo S, Lee J, Kim Y: Characterization of iron- and manganese-containing superoxide dismutase from methyllobacillus Sp. Strain SK1 DSM 8269. Molecules and Cells 2007, 23: 370\u2013378.","journal-title":"Molecules and Cells"},{"key":"2242_CR26","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1007\/s10529-005-4951-3","volume":"28","author":"Z Zheng","year":"2006","unstructured":"Zheng Z, Jiang Y, Miao J, Wang Q, Zhang B, Li G: Purification and characterization of a cold-active iron-superoxide dismutase from a psychrophilic bacterium, Marinomonas sp. NJ522. Biotechnology Letters 2006, 28: 85\u201388. 10.1007\/s10529-005-4951-3","journal-title":"Biotechnology Letters"},{"key":"2242_CR27","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1007\/s00253-006-0834-3","volume":"75","author":"Y He","year":"2007","unstructured":"He Y, Fan K, Jia C, Wang Z, Pan W, Huang L, Yang K, Dong Z: Characterization of a hyperthermostable Fe-superoxide dismutase from hot spring. Applied Microbiology and Biotechnology 2007, 75: 367\u2013376. 10.1007\/s00253-006-0834-3","journal-title":"Applied Microbiology and Biotechnology"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-257.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,2,27]],"date-time":"2024-02-27T00:03:44Z","timestamp":1708992224000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-257"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,6,2]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2242"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-257","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,6,2]]},"assertion":[{"value":"30 November 2007","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2008","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 June 2008","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"257"}}