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Johannes Söding

Johannes Söding

D-Index & Metrics

Biology and Biochemistry

D-Index
68
Citations
52655
World Ranking
7600
National Ranking
556

Overview

Johannes Söding is affiliated with the Max Planck Society in Germany and has contributed extensively to the field of biochemistry, genetics, and molecular biology. Their research primarily focuses on molecular biology with subfields including ecology, plant science, oncology, and genetics. The work emphasizes areas such as genomics and phylogenetic studies, RNA and protein synthesis mechanisms, RNA research and splicing, bacteriophages and microbial interactions, microbial community ecology and physiology, genomics and chromatin dynamics, and protein structure and dynamics.

Johannes Söding has published numerous papers in various venues. Notable recent publications include:

  • Fast and accurate protein structure search with Foldseek, 2023, Nature Biotechnology
  • Protein Sequence Analysis Using the MPI Bioinformatics Toolkit, 2020, Current Protocols in Bioinformatics
  • Fast and accurate protein structure search with Foldseek, 2022, bioRxiv (Cold Spring Harbor Laboratory)
  • MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics, 2020, Microbiome
  • Fast and sensitive taxonomic assignment to metagenomic contigs, 2021, Bioinformatics

The scientist frequently publishes in venues such as bioRxiv (Cold Spring Harbor Laboratory) with 16 papers, Bioinformatics with 4 papers, NAR Genomics and Bioinformatics, Max Planck Digital Library, and Microbiome.

Collaborations constitute a significant part of Söding's academic work. Frequent co-authors include:

  • Milot Mirdita
  • Martin Steinegger
  • Eli Levy Karin
  • Annika Jochheim
  • Salma Sohrabi-Jahromi

Overall, Johannes Söding's research coverage spans core topics of molecular biology. The scientist's output demonstrates engagement in protein structure analysis, gene annotation in metagenomics, and bioinformatics toolkit development.

Best Publications

  • Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

    Fabian Sievers;Andreas Wilm;David Dineen;Toby J Gibson

  • The HHpred interactive server for protein homology detection and structure prediction

    Johannes Söding;Andreas Biegert;Andrei N. Lupas

  • Protein homology detection by HMM--HMM comparison

    Johannes Söding

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

    Martin Steinegger;Johannes Söding

  • HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

    Michael Remmert;Andreas Biegert;Andreas Hauser;Johannes Söding

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

    Lukas Zimmermann;Andrew Stephens;Seung-Zin Nam;David Rau

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

    Martin Steinegger;Martin Steinegger;Markus Meier;Milot Mirdita;Harald Vöhringer;Harald Vöhringer

  • Uniclust databases of clustered and deeply annotated protein sequences and alignments

    Milot Mirdita;Lars von den Driesch;Lars von den Driesch;Clovis Galiez;Maria Jesus Martin

  • Clustering huge protein sequence sets in linear time

    Martin Steinegger;Martin Steinegger;Martin Steinegger;Johannes Söding

  • Protein sequence analysis using the MPI Bioinformatics Toolkit

    Felix Gabler;Seung-Zin Nam;Sebastian Till;Milot Mirdita

  • Uniform transitions of the general RNA polymerase II transcription complex.

    Andreas Mayer;Michael Lidschreiber;Matthias Siebert;Kristin Leike

  • Fast and accurate automatic structure prediction with HHpred

    Andrea Hildebrand;Michael Remmert;Andreas Biegert;Johannes Söding

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

    Milot Mirdita;Martin Steinegger;Martin Steinegger;Johannes Söding

  • CCMpred--fast and precise prediction of protein residue-residue contacts from correlated mutations.

    Stefan Seemayer;Markus Gruber;Johannes Söding

  • 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

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

    Martin Steinegger;Milot Mirdita;Johannes Söding

  • The MPI Bioinformatics Toolkit for protein sequence analysis

    Andreas Biegert;Christian E. Mayer;Michael Remmert;Johannes Söding

  • More than the sum of their parts: on the evolution of proteins from peptides.

    Johannes Söding;Andrei N. Lupas

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

    Jean Paul Armache;Alexander Jarasch;Andreas M. Anger;Elizabeth Villa

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

    Manjunatha R Karpenahalli;Andrei N Lupas;Johannes Söding

Frequent Co-Authors

Andrei N. Lupas
Andrei N. Lupas Max Planck Society
Rudolf Grimm
Rudolf Grimm University of Innsbruck
Patrick Cramer
Patrick Cramer Max Planck Society
Jean Dalibard
Jean Dalibard Collège de France
William Stafford Noble
William Stafford Noble University of Washington
Steven Hahn
Steven Hahn Fred Hutchinson Cancer Research Center
Karl-Peter Hopfner
Karl-Peter Hopfner Ludwig-Maximilians-Universität München
Eric Westhof
Eric Westhof University of Strasbourg
Markus Zweckstetter
Markus Zweckstetter German Center for Neurodegenerative Diseases
Michael Thomm
Michael Thomm University of Regensburg

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