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Comparison of ARM and HEAT protein repeats.
Andrade MA, Petosa C, O'Donoghue SI, Müller CW, Bork P. Andrade MA, et al. J Mol Biol. 2001 May 25;309(1):1-18. doi: 10.1006/jmbi.2001.4624. J Mol Biol. 2001. PMID: 11491282 Review.
Aquaria: simplifying discovery and insight from protein structures.
O'Donoghue SI, Sabir KS, Kalemanov M, Stolte C, Wellmann B, Ho V, Roos M, Perdigão N, Buske FA, Heinrich J, Rost B, Schafferhans A. O'Donoghue SI, et al. Nat Methods. 2015 Feb;12(2):98-9. doi: 10.1038/nmeth.3258. Nat Methods. 2015. PMID: 25633501 No abstract available.
Unexpected features of the dark proteome.
Perdigão N, Heinrich J, Stolte C, Sabir KS, Buckley MJ, Tabor B, Signal B, Gloss BS, Hammang CJ, Rost B, Schafferhans A, O'Donoghue SI. Perdigão N, et al. Among authors: o donoghue si. Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15898-903. doi: 10.1073/pnas.1508380112. Epub 2015 Nov 17. Proc Natl Acad Sci U S A. 2015. PMID: 26578815 Free PMC article.
COMPARTMENTS: unification and visualization of protein subcellular localization evidence.
Binder JX, Pletscher-Frankild S, Tsafou K, Stolte C, O'Donoghue SI, Schneider R, Jensen LJ. Binder JX, et al. Database (Oxford). 2014 Feb 25;2014:bau012. doi: 10.1093/database/bau012. Print 2014. Database (Oxford). 2014. PMID: 24573882 Free PMC article.
Arena3D: visualization of biological networks in 3D.
Pavlopoulos GA, O'Donoghue SI, Satagopam VP, Soldatos TG, Pafilis E, Schneider R. Pavlopoulos GA, et al. BMC Syst Biol. 2008 Nov 28;2:104. doi: 10.1186/1752-0509-2-104. BMC Syst Biol. 2008. PMID: 19040715 Free PMC article.
The PSSH database of alignments between protein sequences and tertiary structures.
Schafferhans A, Meyer JE, O'Donoghue SI. Schafferhans A, et al. Nucleic Acids Res. 2003 Jan 1;31(1):494-8. doi: 10.1093/nar/gkg110. Nucleic Acids Res. 2003. PMID: 12520061 Free PMC article.
The SRS 3D module: integrating structures, sequences and features.
O'Donoghue SI, Meyer JE, Schafferhans A, Fries K. O'Donoghue SI, et al. Bioinformatics. 2004 Oct 12;20(15):2476-8. doi: 10.1093/bioinformatics/bth260. Epub 2004 Apr 15. Bioinformatics. 2004. PMID: 15087318
Adaptation of protein surfaces to subcellular location.
Andrade MA, O'Donoghue SI, Rost B. Andrade MA, et al. J Mol Biol. 1998 Feb 20;276(2):517-25. doi: 10.1006/jmbi.1997.1498. J Mol Biol. 1998. PMID: 9512720
Automated assignment of ambiguous nuclear overhauser effects with ARIA.
Linge JP, O'Donoghue SI, Nilges M. Linge JP, et al. Methods Enzymol. 2001;339:71-90. doi: 10.1016/s0076-6879(01)39310-2. Methods Enzymol. 2001. PMID: 11462826 No abstract available.
Unraveling the symmetry ambiguity in a hexamer: calculation of the R6 human insulin structure.
O'Donoghue SI, Chang X, Abseher R, Nilges M, Led JJ. O'Donoghue SI, et al. J Biomol NMR. 2000 Feb;16(2):93-108. doi: 10.1023/a:1008323819099. J Biomol NMR. 2000. PMID: 10723989
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