Johannes Söding

Publication Activity (10 Years)

Years Active: 2003-2021
Publications (10 Years): 13

Top Topics

Sequence Analysis

Amino Acid Sequences

Protein Structure

Top Venues

Nucleic Acids Res.

PLoS Comput. Biol.

Publications

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) (2021)
Salma Sohrabi-Jahromi, Johannes Söding
Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins. Bioinform. 37 (Supplement) (2021)
Milot Mirdita, Martin Steinegger, Florian P. Breitwieser, Johannes Söding, Eli Levy Karin
Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinform. 37 (18) (2021)
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) (2021)
Milot Mirdita, Martin Steinegger, Johannes Söding
MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinform. 35 (16) (2019)
Nikolaos Papadopoulos, R. Gonzalo Parra, Johannes Söding
PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes. Bioinform. 35 (18) (2019)
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) (2019)
Susann Vorberg, Stefan Seemayer, Johannes Söding
Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction. PLoS Comput. Biol. 14 (11) (2018)
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) (2018)
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) (2017)
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) (2017)
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) (2016)
Maria Hauser, Martin Steinegger, Johannes Söding
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. Bioinform. 32 (9) (2016)
Jessica Andreani, Johannes Söding
-strand pairing from direct coupling patterns. Bioinform. 31 (11) (2015)
Armin Meier, Johannes Söding
Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling. PLoS Comput. Biol. 11 (10) (2015)
Armin Meier, Johannes Söding
Context similarity scoring improves protein sequence alignments in the midnight zone. Bioinform. 31 (5) (2015)
Stefan Seemayer, Markus Gruber, Johannes Söding
CCMpred - fast and precise prediction of protein residue-residue contacts from correlated mutations. Bioinform. 30 (21) (2014)
Matthias Siebert, Johannes Söding
Universality of core promoter elements? Nat. 511 (7510) (2014)
Maria Hauser, Christian E. Mayer, Johannes Söding
kClust: fast and sensitive clustering of large protein sequence databases. BMC Bioinform. 14 (2013)
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) (2012)
Christof Angermüller, Andreas Biegert, Johannes Söding
Discriminative modelling of context-specific amino acid substitution probabilities. Bioinform. 28 (24) (2012)
Michael Remmert, Dirk Linke, Andrei N. Lupas, Johannes Söding
HHomp - prediction and classification of outer membrane proteins. Nucleic Acids Res. 37 (Web-Server-Issue) (2009)
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) (2009)
J. D. Fischer, Christian E. Mayer, Johannes Söding
Prediction of protein functional residues from sequence by probability density estimation. Bioinform. 24 (5) (2008)
Andreas Biegert, Johannes Söding
identification of highly diverged protein repeats by probabilistic consistency. Bioinform. 24 (6) (2008)
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)
Johannes Söding, Michael Remmert, Andreas Biegert
protein repeat detection and the origin of TIM barrels. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
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) (2006)
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) (2006)
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) (2005)
Johannes Söding
Protein homology detection by HMM?CHMM comparison. Bioinform. 21 (7) (2005)
Markus Gruber, Johannes Söding, Andrei N. Lupas
REPPER - repeats and their periodicities in fibrous proteins. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
Johannes Söding, Andrei N. Lupas
0n the Evolution of Proteins from Peptides(Invited Talk). German Conference on Bioinformatics (2003)