Johannes Söding
Johannes Söding
Max-Planck-Institute for Multidisciplinary Sciences, Göttingen
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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega
F Sievers, A Wilm, D Dineen, TJ Gibson, K Karplus, W Li, R Lopez, ...
Molecular systems biology 7 (1), 539, 2011
The HHpred interactive server for protein homology detection and structure prediction
J Söding, A Biegert, AN Lupas
Nucleic acids research 33 (suppl_2), W244-W248, 2005
Protein homology detection by HMM–HMM comparison
J Söding
Bioinformatics 21 (7), 951-960, 2005
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
M Remmert, A Biegert, A Hauser, J Söding
Nature methods 9 (2), 173-175, 2012
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
M Steinegger, J Söding
Nature biotechnology 35 (11), 1026-1028, 2017
A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core
L Zimmermann, A Stephens, SZ Nam, D Rau, J Kübler, M Lozajic, ...
Journal of molecular biology 430 (15), 2237-2243, 2018
HH-suite3 for fast remote homology detection and deep protein annotation
M Steinegger, M Meier, M Mirdita, H Vöhringer, SJ Haunsberger, J Söding
BMC bioinformatics 20, 1-15, 2019
Clustering huge protein sequence sets in linear time
M Steinegger, J Söding
Nature communications 9 (1), 2542, 2018
Fast and accurate protein structure search with Foldseek
M van Kempen, SS Kim, C Tumescheit, M Mirdita, J Lee, CLM Gilchrist, ...
Nature Biotechnology, 1-4, 2023
Uniclust databases of clustered and deeply annotated protein sequences and alignments
M Mirdita, L Von Den Driesch, C Galiez, MJ Martin, J Söding, ...
Nucleic acids research 45 (D1), D170-D176, 2017
Uniform transitions of the general RNA polymerase II transcription complex
A Mayer, M Lidschreiber, M Siebert, K Leike, J Söding, P Cramer
Nature structural & molecular biology 17 (10), 1272-1278, 2010
Protein sequence analysis using the MPI bioinformatics toolkit
F Gabler, SZ Nam, S Till, M Mirdita, M Steinegger, J Söding, AN Lupas, ...
Current Protocols in Bioinformatics 72 (1), e108, 2020
Fast and accurate automatic structure prediction with HHpred
A Hildebrand, M Remmert, A Biegert, J Söding
Proteins: Structure, Function, and Bioinformatics 77 (S9), 128-132, 2009
CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations
S Seemayer, M Gruber, J Söding
Bioinformatics 30 (21), 3128-3130, 2014
The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis
V Alva, SZ Nam, J Söding, AN Lupas
Nucleic acids research 44 (W1), W410-W415, 2016
MMseqs2 desktop and local web server app for fast, interactive sequence searches
M Mirdita, M Steinegger, J Söding
Bioinformatics 35 (16), 2856-2858, 2019
Three-body decay of a rubidium Bose–Einstein condensate
J Söding, D Guéry-Odelin, P Desbiolles, F Chevy, H Inamori, J Dalibard
Applied physics B 69, 257-261, 1999
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
M Steinegger, M Mirdita, J Söding
Nature methods 16 (7), 603-606, 2019
The MPI Bioinformatics Toolkit for protein sequence analysis
A Biegert, C Mayer, M Remmert, J Söding, AN Lupas
Nucleic acids research 34 (suppl_2), W335-W339, 2006
More than the sum of their parts: on the evolution of proteins from peptides
J Söding, AN Lupas
Bioessays 25 (9), 837-846, 2003
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