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ORCIDJohannes Söding
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- affiliation: Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Journal Articles
- 2021
[j32]Milot Mirdita
, Martin Steinegger, Florian P. Breitwieser, Johannes Söding, Eli Levy Karin:
Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinform. 37(18): 3029-3031 (2021)- [j31]Ruoshi Zhang, Milot Mirdita, Eli Levy Karin, Clovis Norroy, Clovis Galiez, Johannes Söding:
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinform. 37(19): 3364-3366 (2021) - [j30]Salma Sohrabi-Jahromi, Johannes Söding:
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. Bioinform. 37(Supplement): 308-316 (2021) - [j29]Bi Zhao, Akila Katuwawala, Christopher J. Oldfield, A. Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz A. Kurgan:
DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Res. 49(Database-Issue): D298-D308 (2021) - 2019
- [j28]Milot Mirdita, Martin Steinegger, Johannes Söding:
MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinform. 35(16): 2856-2858 (2019) - [j27]Nikolaos Papadopoulos, R. Gonzalo Parra, Johannes Söding:
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Bioinform. 35(18): 3517-3519 (2019) - [j26]Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding:
HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinform. 20(1): 473:1-473:15 (2019) - 2018
- [j25]Anja Kiesel, Christian Roth, Wanwan Ge, Maximilian Weß, Markus Meier, Johannes Söding:
The BaMM web server for de-novo motif discovery and regulatory sequence analysis. Nucleic Acids Res. 46(Webserver-Issue): W215-W220 (2018) - [j24]Susann Vorberg, Stefan Seemayer, Johannes Söding:
Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Comput. Biol. 14(11) (2018) - 2017
- [j23]Clovis Galiez, Matthias Siebert, François Enault, Jonathan Vincent, Johannes Söding:
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. Bioinform. 33(19): 3113-3114 (2017) - [j22]Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria Jesus Martin, Johannes Söding, Martin Steinegger:
Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Res. 45(Database-Issue): D170-D176 (2017) - 2016
- [j21]Maria Hauser, Martin Steinegger, Johannes Söding:
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinform. 32(9): 1323-1330 (2016) - [j20]Vikram Alva, Seung-Zin Nam, Johannes Söding, Andrei N. Lupas:
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res. 44(Webserver-Issue): W410-W415 (2016) - 2015
- [j19]Armin Meier, Johannes Söding:
Context similarity scoring improves protein sequence alignments in the midnight zone. Bioinform. 31(5): 674-681 (2015) - [j18]Jessica Andreani, Johannes Söding:
bbcontacts: prediction of β-strand pairing from direct coupling patterns. Bioinform. 31(11): 1729-1737 (2015) - [j17]Armin Meier, Johannes Söding:
Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling. PLoS Comput. Biol. 11(10) (2015) - 2014
- [j16]Stefan Seemayer, Markus Gruber, Johannes Söding:
CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinform. 30(21): 3128-3130 (2014) - [j15]Matthias Siebert, Johannes Söding:
Universality of core promoter elements? Nat. 511(7510): E11-E12 (2014) - 2013
- [j14]Maria Hauser, Christian E. Mayer, Johannes Söding:
kClust: fast and sensitive clustering of large protein sequence databases. BMC Bioinform. 14: 248 (2013) - 2012
- [j13]Christof Angermüller, Andreas Biegert, Johannes Söding:
Discriminative modelling of context-specific amino acid substitution probabilities. Bioinform. 28(24): 3240-3247 (2012) - [j12]Sebastian Luehr, Holger Hartmann, Johannes Söding:
The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences. Nucleic Acids Res. 40(Web-Server-Issue): 104-109 (2012) - 2009
- [j11]Alex Bateman, Robert D. Finn, Peter J. Sims, Therese Wiedmer, Andreas Biegert, Johannes Söding:
Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. Bioinform. 25(2): 159-162 (2009) - [j10]Michael Remmert, Dirk Linke, Andrei N. Lupas, Johannes Söding:
HHomp - prediction and classification of outer membrane proteins. Nucleic Acids Res. 37(Web-Server-Issue): 446-451 (2009) - 2008
- [j9]J. D. Fischer, Christian E. Mayer, Johannes Söding:
Prediction of protein functional residues from sequence by probability density estimation. Bioinform. 24(5): 613-620 (2008) - [j8]Andreas Biegert, Johannes Söding:
De novo identification of highly diverged protein repeats by probabilistic consistency. Bioinform. 24(6): 807-814 (2008) - 2007
- [j7]Manjunatha R. Karpenahalli, Andrei N. Lupas, Johannes Söding:
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. BMC Bioinform. 8 (2007) - 2006
- [j6]Johannes Söding, Michael Remmert, Andreas Biegert:
HHrep: de novo protein repeat detection and the origin of TIM barrels. Nucleic Acids Res. 34(Web-Server-Issue): 137-142 (2006) - [j5]Andreas Biegert, Christian E. Mayer, Michael Remmert, Johannes Söding, Andrei N. Lupas:
The MPI Bioinformatics Toolkit for protein sequence analysis. Nucleic Acids Res. 34(Web-Server-Issue): 335-339 (2006) - [j4]Johannes Söding, Michael Remmert, Andreas Biegert, Andrei N. Lupas:
HHsenser: exhaustive transitive profile search using HMM-HMM comparison. Nucleic Acids Res. 34(Web-Server-Issue): 374-378 (2006) - 2005
- [j3]Johannes Söding:
Protein homology detection by HMM?CHMM comparison. Bioinform. 21(7): 951-960 (2005) - [j2]Markus Gruber, Johannes Söding, Andrei N. Lupas:
REPPER - repeats and their periodicities in fibrous proteins. Nucleic Acids Res. 33(Web-Server-Issue): 239-243 (2005) - [j1]Johannes Söding, Andreas Biegert, Andrei N. Lupas:
The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res. 33(Web-Server-Issue): 244-248 (2005)
Conference and Workshop Papers
- 2003
- [c1]Johannes Söding, Andrei N. Lupas:
0n the Evolution of Proteins from Peptides(Invited Talk). German Conference on Bioinformatics 2003: 95-96
Coauthor Index
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