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Items: 13

1.

Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome.

Hücker SM, Ardern Z, Goldberg T, Schafferhans A, Bernhofer M, Vestergaard G, Nelson CW, Schloter M, Rost B, Scherer S, Neuhaus K.

PLoS One. 2017 Sep 13;12(9):e0184119. doi: 10.1371/journal.pone.0184119. eCollection 2017.

2.

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC).

Neuhaus K, Landstorfer R, Fellner L, Simon S, Schafferhans A, Goldberg T, Marx H, Ozoline ON, Rost B, Kuster B, Keim DA, Scherer S.

BMC Genomics. 2016 Feb 24;17:133. doi: 10.1186/s12864-016-2456-1.

3.

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.

Proc Natl Acad Sci U S A. 2015 Dec 29;112(52):15898-903. doi: 10.1073/pnas.1508380112. Epub 2015 Nov 17.

4.

Tools and data services registry: a community effort to document bioinformatics resources.

Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.

Nucleic Acids Res. 2016 Jan 4;44(D1):D38-47. doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3.

5.

Integrated visual analysis of protein structures, sequences, and feature data.

Stolte C, Sabir KS, Heinrich J, Hammang CJ, Schafferhans A, O'Donoghue SI.

BMC Bioinformatics. 2015;16 Suppl 11:S7. doi: 10.1186/1471-2105-16-S11-S7. Epub 2015 Aug 13.

6.

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.

Nat Methods. 2015 Feb;12(2):98-9. doi: 10.1038/nmeth.3258. No abstract available.

PMID:
25633501
7.

Taking structure searches to the next dimension.

Schafferhans A, Rost B.

Structure. 2014 Jul 8;22(7):938-9. doi: 10.1016/j.str.2014.06.007.

8.

PredictProtein--an open resource for online prediction of protein structural and functional features.

Yachdav G, Kloppmann E, Kajan L, Hecht M, Goldberg T, Hamp T, Hönigschmid P, Schafferhans A, Roos M, Bernhofer M, Richter L, Ashkenazy H, Punta M, Schlessinger A, Bromberg Y, Schneider R, Vriend G, Sander C, Ben-Tal N, Rost B.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W337-43. doi: 10.1093/nar/gku366. Epub 2014 May 5.

9.

Visualization of macromolecular structures.

O'Donoghue SI, Goodsell DS, Frangakis AS, Jossinet F, Laskowski RA, Nilges M, Saibil HR, Schafferhans A, Wade RC, Westhof E, Olson AJ.

Nat Methods. 2010 Mar;7(3 Suppl):S42-55. doi: 10.1038/nmeth.1427. Epub 2010 Mar 1. Review.

PMID:
20195256
10.

The SRS 3D module: integrating structures, sequences and features.

O'Donoghue SI, Meyer JE, Schafferhans A, Fries K.

Bioinformatics. 2004 Oct 12;20(15):2476-8. Epub 2004 Apr 15.

PMID:
15087318
11.

The PSSH database of alignments between protein sequences and tertiary structures.

Schafferhans A, Meyer JE, O'Donoghue SI.

Nucleic Acids Res. 2003 Jan 1;31(1):494-8.

12.

Peptide/benzodiazepine hybrids as ligands of CCK(A) and CCK(B) receptors.

Escherich A, Lutz J, Escrieut C, Fourmy D, van Neuren AS, Müller G, Schafferhans A, Klebe G, Moroder L.

Biopolymers. 2000-2001;56(2):55-76.

PMID:
11592053
13.

Docking ligands onto binding site representations derived from proteins built by homology modelling.

Schafferhans A, Klebe G.

J Mol Biol. 2001 Mar 16;307(1):407-27.

PMID:
11243828

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