0n the Evolution of Proteins from Peptides(Invited Talk). - Johannes Söding; Andrei N. Lupas (German Conference on Bioinformatics, 2003)

Protein homology detection by HMM?CHMM comparison. - Johannes Söding (Bioinform., 2005)

REPPER - repeats and their periodicities in fibrous proteins. - Markus Gruber; Johannes Söding; Andrei N. Lupas (Nucleic Acids Res., 2005)

The HHpred interactive server for protein homology detection and structure prediction. - Johannes Söding; Andreas Biegert; Andrei N. Lupas (Nucleic Acids Res., 2005)

The MPI Bioinformatics Toolkit for protein sequence analysis. - Andreas Biegert; Christian E. Mayer; Michael Remmert; Johannes Söding; Andrei N. Lupas (Nucleic Acids Res., 2006)

HHrep: de novo protein repeat detection and the origin of TIM barrels. - Johannes Söding; Michael Remmert; Andreas Biegert (Nucleic Acids Res., 2006)

HHsenser: exhaustive transitive profile search using HMM-HMM comparison. - Johannes Söding; Michael Remmert; Andreas Biegert; Andrei N. Lupas (Nucleic Acids Res., 2006)

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. - Manjunatha R. Karpenahalli; Andrei N. Lupas; Johannes Söding (BMC Bioinform., 2007)

De novo identification of highly diverged protein repeats by probabilistic consistency. - Andreas Biegert; Johannes Söding (Bioinform., 2008)

Prediction of protein functional residues from sequence by probability density estimation. - J. D. Fischer; Christian E. Mayer; Johannes Söding (Bioinform., 2008)

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors. - Alex Bateman; Robert D. Finn; Peter J. Sims; Therese Wiedmer; Andreas Biegert; Johannes Söding (Bioinform., 2009)

HHomp - prediction and classification of outer membrane proteins. - Michael Remmert; Dirk Linke; Andrei N. Lupas; Johannes Söding (Nucleic Acids Res., 2009)

Discriminative modelling of context-specific amino acid substitution probabilities. - Christof Angermüller; Andreas Biegert; Johannes Söding (Bioinform., 2012)

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences. - Sebastian Luehr; Holger Hartmann; Johannes Söding (Nucleic Acids Res., 2012)

kClust: fast and sensitive clustering of large protein sequence databases. - Maria Hauser; Christian E. Mayer; Johannes Söding (BMC Bioinform., 2013)

CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations. - Stefan Seemayer; Markus Gruber; Johannes Söding (Bioinform., 2014)

Universality of core promoter elements? - Matthias Siebert; Johannes Söding (Nat., 2014)

bbcontacts: prediction of β-strand pairing from direct coupling patterns. - Jessica Andreani; Johannes Söding (Bioinform., 2015)

Context similarity scoring improves protein sequence alignments in the midnight zone. - Armin Meier; Johannes Söding (Bioinform., 2015)

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling. - Armin Meier; Johannes Söding (PLoS Comput. Biol., 2015)

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. - Maria Hauser; Martin Steinegger; Johannes Söding (Bioinform., 2016)

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. - Vikram Alva; Seung-Zin Nam; Johannes Söding; Andrei N. Lupas (Nucleic Acids Res., 2016)

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs. - Clovis Galiez; Matthias Siebert; François Enault; Jonathan Vincent; Johannes Söding (Bioinform., 2017)

Uniclust databases of clustered and deeply annotated protein sequences and alignments. - Milot Mirdita; Lars von den Driesch; Clovis Galiez; Maria Jesus Martin; Johannes Söding; Martin Steinegger (Nucleic Acids Res., 2017)

The BaMM web server for de-novo motif discovery and regulatory sequence analysis. - Anja Kiesel; Christian Roth 005; Wanwan Ge; Maximilian Weß; Markus Meier; Johannes Söding (Nucleic Acids Res., 2018)

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. - Susann Vorberg; Stefan Seemayer; Johannes Söding (PLoS Comput. Biol., 2018)

MMseqs2 desktop and local web server app for fast, interactive sequence searches. - Milot Mirdita; Martin Steinegger; Johannes Söding (Bioinform., 2019)

PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. - Nikolaos Papadopoulos; R. Gonzalo Parra; Johannes Söding (Bioinform., 2019)

HH-suite3 for fast remote homology detection and deep protein annotation. - Martin Steinegger; Markus Meier; Milot Mirdita; Harald Vöhringer; Stephan J. Haunsberger; Johannes Söding (BMC Bioinform., 2019)

Fast and sensitive taxonomic assignment to metagenomic contigs. - Milot Mirdita; Martin Steinegger; Florian P. Breitwieser; Johannes Söding; Eli Levy Karin (Bioinform., 2021)

Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. - Salma Sohrabi-Jahromi; Johannes Söding (Bioinform., 2021)

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. - Ruoshi Zhang; Milot Mirdita; Eli Levy Karin; Clovis Norroy; Clovis Galiez; Johannes Söding (Bioinform., 2021)

DescribePROT: database of amino acid-level protein structure and function predictions. - 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; et al. (Nucleic Acids Res., 2021)