Publications

53.

Journal Article

Siebert, M.; Söding, J.: Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences. Nucleic Acids Research 44 (13), pp. 6055 - 6069 (2016)

MPG.PuRe

54.

Journal Article

Alva, V.; Nam, S. Z.; Söding, J.; Lupas, A. N.: The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Research 44 (W1), pp. W410 - W415 (2016)

MPG.PuRe

55.

Journal Article

Hauser, M.; Steinegger, M.; Söding, J.: MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinformatics 32 (9), pp. 1323 - 1330 (2016)

MPG.PuRe

56.

Journal Article

Stützer, A.; Liokatis, S.; Kiesel, A.; Schwarzer, D.; Sprangers, R.; Söding, J.; Selenko, P.; Fischle, W.: Modulations of DNA contacts by linker histones and post-translational modifications determine the mobility and modifiability of nucleosomal H3 tails. Molecular Cell 61 (2), pp. 247 - 259 (2016)

MPG.PuRe

57.

Journal Article

Alva, V.; Söding, J.; Lupas, A. N.: A vocabulary of ancient peptides at the origin of folded proteins. eLife 4, e09410 (2015)

MPG.PuRe

58.

Journal Article

Meier, A.; Söding, J.: Automatic prediction of protein 3D Structures by probabilistic multi-template homology modeling. PLoS Computational Biology 11 (10), e1004343 (2015)

MPG.PuRe

59.

Journal Article

Mühlbacher, W.; Mayer, A.; Sun, M.; Remmert, M.; Cheung, A. C. M.; Niesser, J.; Söding, J.; Cramer, P.: Structure of Ctk3, a subunit of the RNA polymerase II CTD kinase complex, reveals a non-canonical CTD-interacting domain fold. Proteins: Structure, Function, and Bioinformatics 83 (10), pp. 1849 - 1858 (2015)

MPG.PuRe

60.

Journal Article

Meier, A.; Söding, J.: Context similarity scoring improves protein sequence alignments in the midnight zone. Bioinformatics 31 (5), pp. 674 - 681 (2015)

MPG.PuRe

61.

Journal Article

Andreani, J.; Söding, J.: bbcontacts: Prediction of β-strand pairing from direct coupling patterns. Bioinformatics 31 (11), pp. 1729 - 1737 (2015)

MPG.PuRe

62.

Journal Article

Seemayer, S.; Gruber, M.; Söding, J.: CCMpred-fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinformatics 30 (21), pp. 3128 - 3130 (2014)

MPG.PuRe

63.

Journal Article

Bäjen, C.; Torkler, P.; Gressel, S.; Essig, K.; Söding, J.; Cramer, P.: Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition. Molecular Cell 55 (5), pp. 745 - 757 (2014)

MPG.PuRe

64.

Journal Article

Siebert, M.; Söding, J.: Universality of core promoter elements? Nature 511 (7510), pp. E11 - E12 (2014)

MPG.PuRe

65.

Journal Article

Wickles, S.; Singharoy, A.; Andreani, J.; Seemayer, S.; Bischoff, L.; Berninghausen, O.; Söding, J.; Schulten, K.; van der Sluis, E. O.; Beckmann, R.: A structural model of the active ribosome-bound membrane protein insertase YidC. eLife 3, e03035 (2014)

MPG.PuRe

66.

Journal Article

Saponaro, M.; Mitter, R.; Kantidakis, T.; Kelly, G. P.; Heron, M.; Williams, H.; Söding, J.; Stewart, A.; Svejstrup, J. Q.: RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress. Cell 157 (5), pp. 1037 - 1049 (2014)

MPG.PuRe

67.

Journal Article

Runge, S.; Sparrer, K. M. J.; Lässig, C.; Hembach, K.; Baum, A.; Garcia-Sastre, A.; Söding, J.; Conzelmann, K. K.; Hopfner, K. P.: In vivo ligands of MDA5 and RIG-I in measles virus-infected cells. PLoS Pathogens 10 (4), e1004081 (2014)

MPG.PuRe

68.

Journal Article

Söding, J.: In silico-Funktions- und Strukturvorhersagen bei Proteinen. BIOspektrum 20 (2), pp. 158 - 160 (2014)

MPG.PuRe

69.

Journal Article

Meinel, D. M.; Burkert-Kautzsch, C.; Kieser, A.; O'Duibhir, E.; Siebert, M.; Mayer, A.; Cramer, P.; Söding, J.; Holstege, F. C.; Sträßer, K.: Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II. PLoS Genetics 9 (11), e1003914 (2013)

MPG.PuRe

70.

Journal Article

Schulz, D.; Schwalb, B.; Kiesel, A.; Baejen, C.; Torkler, P.; Gagneur, J.; Söding, J.; Cramer, P.: Transcriptome surveillance by selective termination of noncoding RNA synthesis. Cell 155 (5), pp. 1075 - 1087 (2013)

MPG.PuRe

71.

Journal Article

Hauser, M.; Mayer, C. E.; Söding, J.: kClust: Fast and sensitive clustering of large protein sequence databases. BMC Bioinformatics 14, 248 (2013)

MPG.PuRe

72.

Journal Article

Hartmann, H.; Guthoehrlein, E. W.; Siebert, M.; Luehr, S.; Söding, J.: P-value-based regulatory motif discovery using positional weight matrices. Genome Research 23 (1), pp. 181 - 194 (2013)

MPG.PuRe

73.

Journal Article

Tischer, S.; Reineck, M.; Söding, J.; Münder, S.; Böttger, A.: Eph receptors and ephrin class B ligands are expressed at tissue boundaries in Hydra vulgaris. The International Journal of Develomental Biology 57, pp. 759 - 765 (2013)

MPG.PuRe

74.

Journal Article

Angermueller, C.; Biegert, A.; Söding, J.: Discriminative modelling of context-specific amino acid substitution probabilities. Bioinformatics 28 (24), pp. 3240 - 3247 (2012)

MPG.PuRe

75.

Journal Article

Close, P.; East, P.; Dirac-Svejstrup, A. B.; Hartmann, H.; Heron, M.; Maslen, S.; Chariot, A.; Söding, J.; Skehel, M.; Svejstrup, J. Q.: DBIRD complex integrates alternative mRNA splicing with RNA polymerase II transcript elongation. Nature 484 (7394), pp. 386 - 389 (2012)

MPG.PuRe

76.

Journal Article

Feller, C.; Prestel, M.; Hartmann, H.; Straub, T.; Söding, J.; Becker, P. B.: The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset. Nucleic Acids Research 40 (4), pp. 1509 - 1522 (2012)

MPG.PuRe

77.

Journal Article

Luehr, S.; Hartmann, H.; Söding, J.: The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences. Nucleic Acids Research 40 (W1), pp. W104 - W109 (2012)

MPG.PuRe

78.

Journal Article

Remmert, M.; Biegert, A.; Hauser, A.; Söding, J.: HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods 9 (2), pp. 173 - 175 (2012)

MPG.PuRe

79.

Journal Article

Seizl, M.; Hartmann, H.; Hoeg, F.; Kurth, F.; Martin, D. E.; Söding, J.; Cramer, P.: A conserved GA element in TATA-less RNA polymerase II promoters. PLoS One 6 (11), e27595 (2011)

MPG.PuRe

80.

Journal Article

Sievers, F.; Wilm, A.; Dineen, D.; Gibson, T. J.; Karplus, K.; Li, W.; Lopez, R.; McWilliam, H.; Remmert, M.; Söding, J. et al.; Thompson, J. D.; Higgins, D. G.: Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7, 539 (2011)

MPG.PuRe

81.

Journal Article

Söding, J.; Remmert, M.: Protein sequence comparison and fold recognition: progress and good-practice benchmarking. Current Opinion in Structural Biology 21 (3), pp. 404 - 411 (2011)

MPG.PuRe

82.

Journal Article

Frauer, C.; Rottach, A.; Meilinger, D.; Bultmann, S.; Fellinger, K.; Hasenoeder, S.; Wang, M.; Qin, W.; Söding, J.; Spada, F. et al.; Leonhardt, H.: Different binding properties and function of CXXC zinc finger domains in Dnmt1 and Tet1. PLoS One 6 (2), e16627 (2011)

MPG.PuRe

83.

Journal Article

Lammens, K.; Bemeleit, D. J.; Moeckel, C.; Clausing, E.; Schele, A.; Hartung, S.; Schiller, C. B.; Lucas, M.; Angermueller, C.; Söding, J. et al.; Straesser, K.; Hopfner, K. P.: The Mre11:Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair. Cell 145 (1), pp. 54 - 66 (2011)

MPG.PuRe

84.

Journal Article

Armache, J. P.; Jarasch, A.; Anger, A. M.; Villa, E.; Becker, T.; Bhushan, S.; Jossinet, F.; Habeck, M.; Dindar, G.; Franckenberg, S. et al.; Marquez, V.; Mielke, T.; Thomm, M.; Berninghausen, O.; Beatrix, B.; Söding, J.; Westhof, E.; Wilson, D. N.; Beckmann, R.: Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-angstrom resolution. Proceedings of the National Academy of Sciences of the United States of America 107 (46), pp. 19748 - 19753 (2010)

MPG.PuRe

85.

Journal Article

Armache, J. P.; Jarasch, A.; Anger, A. M.; Villa, E.; Becker, T.; Bhushan, S.; Jossinet, F.; Habeck, M.; Dindar, G.; Franckenberg, S. et al.; Marquez, V.; Mielke, T.; Thomm, M.; Berninghausen, O.; Beatrix, B.; Söding, J.; Westhof, E.; Wilson, D. N.; Beckmann, R.: Localization of eukaryote-specific ribosomal proteins in a 5.5-angstrom cryo-EM map of the 80S eukaryotic ribosome. Proceedings of the National Academy of Sciences of the United States of America 107 (46), pp. 19754 - 19759 (2010)

MPG.PuRe

86.

Journal Article

Graebsch, A.; Roche, S.; Kostrewa, D.; Söding, J.; Niessing, D.: Of bits and bugs - On the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure. PLoS One 5 (10), e13402 (2010)

MPG.PuRe

87.

Journal Article

Mayer, A.; Lidschreiber, M.; Siebert, M.; Leike, K.; Söding, J.; Cramer, P.: Uniform transitions of the general RNA polymerase II transcription complex. Nature Structural and Molecular Biology 17 (10), pp. 1272 - 1278 (2010)

MPG.PuRe

88.

Journal Article

Alva, V.; Remmert, M.; Biegert, A.; Lupas, A. N.; Söding, J.: A galaxy of folds. Protein Science 19 (1), pp. 124 - 130 (2010)

MPG.PuRe

89.

Journal Article

Lasi, M.; Pauly, B.; Schmidt, N.; Cikala, M.; Stiening, B.; Kaesbauer, T.; Zenner, G.; Popp, T.; Wagner, A.; Knapp, R. T. et al.; Huber, A. H.; Grunert, M.; Söding, J.; David, C. N.; Boettger, A.: The molecular cell death machinery in the simple cnidarian Hydra includes an expanded caspase family and pro- and anti-apoptotic Bcl-2 proteins. Cell Research 20 (7), pp. 812 - 825 (2010)

MPG.PuRe

90.

Journal Article

Remmert, M.; Biegert, A.; Linke, D.; Lupas, A. N.; Soeding, J.: Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin. Molecular Biology and Evolution 27 (6), pp. 1348 - 1358 (2010)

MPG.PuRe

91.

Journal Article

Biegert, A.; Söding, J.: Sequence context-specific profiles for homology searching. Proceedings of the National Academy of Sciences of the United States of America 106 (10), pp. 3770 - 3775 (2009)

MPG.PuRe

92.

Journal Article

Bateman, A.; Finn, R. D.; Sims, P. J.; Wiedmer, T.; Biegert, A.; Söding, J.: Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bioinformatics 25 (2), pp. 159 - 162 (2009)

MPG.PuRe

93.

Journal Article

Biegert, A.; Söding, J.: A boost for sequence searching. G.I.T. Laboratory Journal 9-10, pp. 22 - 23 (2009)

MPG.PuRe

Full

94.

Journal Article

Hildebrand, A.; Remmert, M.; Biegert, A.; Söding, J.: Fast and accurate automatic structure prediction with HHpred. Proteins: Structure, Function, and Bioinformatics 77 (S9), pp. 128 - 132 (2009)

MPG.PuRe

95.

Journal Article

Remmert, M.; Linke, D.; Lupas, A. N.; Söding, J.: HHomp-prediction and classification of outer membrane proteins. Nucleic Acids Research 37 (Suppl. 2), pp. W446 - W451 (2009)

MPG.PuRe

96.

Journal Article

Agarwal, V.; Remmert, M.; Biegert, A.; Söding, J.: PDBalert: Automatic, recurrent remote homology tracking and protein structure prediction. BMC Structural Biology 8, 51 (2008)

MPG.PuRe

97.

Journal Article

Jasiak, A. J.; Hartmann, H.; Karakasili, E.; Kalocsay, M.; Flatley, A.; Kremmer, E.; Strässer, K.; Martin, D. E.; Söding, J.; Cramer, P.: Genome-associated RNA polymerase II includes the dissociable Rpb4/7 subcomplex. The Journal of Biological Chemistry 283, pp. 26423 - 26427 (2008)

MPG.PuRe

98.

Journal Article

Chaudhuri, I.; Söding, J.; Lupas, A. N.: Evolution of the beta-propeller fold. Proteins: Structure, Function, and Bioinformatics 71 (2), pp. 795 - 803 (2008)

MPG.PuRe

99.

Journal Article

Biegert, A.; Söding, J.: De novo identification of highly diverged protein repeats by probabilistic consistency. Bioinformatics 24 (6), pp. 807 - 814 (2008)

MPG.PuRe

100.

Journal Article

Fischer, J. D.; Mayer, C. E.; Söding, J.: Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 24 (5), pp. 613 - 620 (2008)

MPG.PuRe