Johannes Söding

发表

Bayesian Markov models improve the prediction of binding motifs beyond first order

Wanwan Ge, Markus Meier, Christian Roth, 2020, bioRxiv.

Protein homology detection by HMM?CHMM comparison

Johannes Söding, J. Söding, 2005, Bioinform..

REPPER—repeats and their periodicities in fibrous proteins

Markus Gruber, Johannes Söding, Andrei N. Lupas, 2005, Nucleic Acids Res..

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs

Jonathan Vincent, Johannes Söding, Clovis Galiez, 2017, Bioinform..

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences

Johannes Söding, Andrei N. Lupas, Manjunatha R. Karpenahalli, 2007, BMC Bioinformatics.

Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling

Johannes Söding, Armin Meier, J. Söding, 2015, PLoS Comput. Biol..

CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

Markus Gruber, Johannes Söding, Stefan Seemayer, 2014, Bioinform..

PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes

Johannes Söding, Nikolaos Papadopoulos, R Gonzalo Parra, 2018, bioRxiv.

Fast and accurate automatic structure prediction with HHpred

Johannes Söding, Michael Remmert, Andrea Hildebrand, 2009, Proteins.

HHrep: de novo protein repeat detection and the origin of TIM barrels

Johannes Söding, Michael Remmert, Andreas Biegert, 2006, Nucleic Acids Res..

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

Johannes Söding, Felix Gabler, Seung-Zin Nam, 2020, Current protocols in bioinformatics.

Discriminative modelling of context-specific amino acid substitution probabilities

Johannes Söding, Andreas Biegert, Christof Angermüller, 2012, Bioinform..

Phospholipid scramblases and Tubby-like proteins belong to a new superfamily of membrane tethered transcription factors

Robert D. Finn, Alex Bateman, Johannes Söding, 2008, Bioinform..

Clustering huge protein sequence sets in linear time

Johannes Söding, Martin Steinegger, 2018 .

The HHpred interactive server for protein homology detection and structure prediction

Johannes Söding, Andrei N. Lupas, Andreas Biegert, 2005, Nucleic Acids Res..

HHomp—prediction and classification of outer membrane proteins

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2009, Nucleic Acids Res..

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets

Johannes Söding, Martin Steinegger, Maria Hauser, 2016, Bioinform..

0n the Evolution of Proteins from Peptides(Invited Talk)

Johannes Söding, Andrei N. Lupas, 2003, German Conference on Bioinformatics.

The MPI Bioinformatics Toolkit for protein sequence analysis

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2006, Nucleic Acids Res..

Bbcontacts: Prediction of Β-strand Pairing from Direct Coupling Patterns

Johannes Söding, Jessica Andreani, J. Söding, 2015, Bioinform..

The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

Johannes Söding, Andrei N. Lupas, Seung-Zin Nam, 2016, Nucleic Acids Res..

kClust: fast and sensitive clustering of large protein sequence databases

Johannes Söding, Christian E. Mayer, Maria Hauser, 2013, BMC Bioinformatics.

Universality of core promoter elements?

Johannes Söding, Matthias Siebert, J. Söding, 2014, Nature.

Johannes Söding, Armin Meier, 2015, Bioinform..

Prediction of protein functional residues from sequence by probability density estimation

Johannes Söding, Christian E. Mayer, J. D. Fischer, 2008, Bioinform..

HH-suite3 for fast remote homology detection and deep protein annotation

Johannes Söding, Milot Mirdita, Martin Steinegger, 2019, BMC Bioinformatics.

Uniclust databases of clustered and deeply annotated protein sequences and alignments

Maria Jesus Martin, Johannes Söding, Clovis Galiez, 2016, Nucleic Acids Res..

Comparative analysis of coiled-coil prediction methods.

Johannes Söding, Andrei N Lupas, Markus Gruber, 2006, Journal of structural biology.

Linclust: clustering billions of protein sequences per day on a single server

Johannes Söding, Martin Steinegger, 2017 .

MMseqs2 desktop and local web server app for fast, interactive sequence searches

Johannes Söding, Milot Mirdita, Martin Steinegger, 2018 .

The XXmotif web server for eXhaustive, weight matriX-based motif discovery in nucleotide sequences

Johannes Söding, Holger Hartmann, Sebastian Luehr, 2012, Nucleic Acids Res..

MMseqs2: sensitive protein sequence searching for the analysis of massive data sets

Johannes Söding, Martin Steinegger, J. Söding, 2017, bioRxiv.

A boost for sequence searching.

Johannes Söding, Andreas Biegert, 2009 .

De novo identification of highly diverged protein repeats by probabilistic consistency

Johannes Söding, Andreas Biegert, A. Biegert, 2008, Bioinform..

The BaMM web server for de-novo motif discovery and regulatory sequence analysis

Wanwan Ge, Johannes Söding, Christian Roth, 2018, Nucleic Acids Res..

PDBalert: automatic, recurrent remote homology tracking and protein structure prediction

Johannes Söding, Michael Remmert, Vatsal Agarwal, 2008, BMC Structural Biology.

Synthetic protein alignments by CCMgen quantify noise in residue-residue contact prediction

Johannes Söding, Stefan Seemayer, Susann Vorberg, 2018, PLoS Comput. Biol..

HHsenser: exhaustive transitive profile search using HMM–HMM comparison

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2006, Nucleic Acids Res..

A Completely Reimplemented MPI Bioinformatics Toolkit with a New HHpred Server at its Core.

Lukas Zimmermann, Johannes Söding, Felix Gabler, 2017, Journal of molecular biology.

Clustering huge protein sequence sets in linear time

Johannes Söding, Martin Steinegger, J. Söding, 2017, Nature Communications.

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Adam Liwo, Yi He, Jilong Li, 2018, Scientific Reports.

New algorithms and tools for large-scale sequence analysis of metagenomic data

Johannes Söding, Milot Mirdita, Martin Steinegger, 2019 .

Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

Johannes Söding, Salma Sohrabi-Jahromi, 2021, Bioinform..

SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts

Johannes Söding, Eli Levy Karin, Clovis Galiez, 2021, Bioinform..

DescribePROT: database of amino acid-level protein structure and function predictions

A Keith Dunker, Zoran Obradovic, Lukasz Kurgan, 2020, Nucleic Acids Res..

A galaxy of folds

Johannes Söding, Michael Remmert, Andreas Biegert, 2009, Protein science : a publication of the Protein Society.

Different Binding Properties and Function of CXXC Zinc Finger Domains in Dnmt1 and Tet1

Johannes Söding, Heinrich Leonhardt, Weihua Qin, 2011, PloS one.

Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution

Johannes Söding, Michael Habeck, Eric Westhof, 2010, Proceedings of the National Academy of Sciences.

Bayesian multiple logistic regression for case-control GWAS

Johannes Söding, Heribert Schunkert, Saikat Banerjee, 2018, PLoS genetics.

AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-psi beta barrels.

Johannes Söding, Sergej Djuranovic, Vincent Truffault, 2005, Structure.

Genome-associated RNA Polymerase II Includes the Dissociable Rpb4/7 Subcomplex*

Johannes Söding, Holger Hartmann, Patrick Cramer, 2008, Journal of Biological Chemistry.

Evolution of Outer Membrane b-Barrels from an Ancestral bb Hairpin

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2010 .

Bayesian Markov models consistently outperform PWMs at predicting motifs in nucleotide sequences

Johannes Söding, J. Söding, M. Siebert, 2016, bioRxiv.

Evolution of the β‐propeller fold

Johannes Söding, Andrei N. Lupas, J. Söding, 2008, Proteins.

Evolution of Outer Membrane -Barrels from an Ancestral Hairpin

Johannes Söding, Michael Remmert, Andrei N. Lupas, 2010 .

On the origin of the histone fold

Johannes Söding, Andrei N Lupas, Vikram Alva, 2007, BMC Structural Biology.

Big-data approaches to protein structure prediction

Johannes Söding, J. Söding, 2017, Science.

Uniform transitions of the general RNA polymerase II transcription complex

Johannes Söding, Patrick Cramer, Michael Lidschreiber, 2010, Nature Structural &Molecular Biology.

Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold

Johannes Söding, Milot Mirdita, Martin Steinegger, 2018, Nature Methods.

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

Johannes Söding, Milot Mirdita, J. Söding, 2020, Microbiome.

Transcriptome maps of mRNP biogenesis factors define pre-mRNA recognition.

Johannes Söding, Patrick Cramer, Phillipp Torkler, 2014, Molecular cell.

Protein sequence comparison and fold recognition: progress and good-practice benchmarking.

Johannes Söding, Michael Remmert, J. Söding, 2011, Current opinion in structural biology.

Linclust: clustering protein sequences in linear time

Johannes Söding, Martin Steinegger, 2017 .