Articles with public access mandates - Johannes SödingLearn more
Available somewhere: 74
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
Mandates: Science Foundation Ireland
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
M Steinegger, J Söding
Nature biotechnology 35 (11), 1026-1028, 2017
Mandates: European Commission, Federal Ministry of Education and Research, Germany
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
Mandates: German Research Foundation
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
Mandates: European Commission
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
Mandates: Federal Ministry of Education and Research, Germany
Clustering huge protein sequence sets in linear time
M Steinegger, J Söding
Nature communications 9 (1), 2542, 2018
Mandates: US Department of Energy, European Commission
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
Mandates: European Commission, Federal Ministry of Education and Research, Germany
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
Mandates: German Research Foundation
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
Mandates: German Research Foundation
MMseqs2 desktop and local web server app for fast, interactive sequence searches
M Mirdita, M Steinegger, J Söding
Bioinformatics 35 (16), 2856-2858, 2019
Mandates: European Commission
Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
M Steinegger, M Mirdita, J Söding
Nature methods 16 (7), 603-606, 2019
Mandates: European Commission
Cryo-EM structure and rRNA model of a translating eukaryotic 80S ribosome at 5.5-Å resolution
JP Armache, A Jarasch, AM Anger, E Villa, T Becker, S Bhushan, ...
Proceedings of the National Academy of Sciences 107 (46), 19748-19753, 2010
Mandates: German Research Foundation
Transcriptome surveillance by selective termination of noncoding RNA synthesis
D Schulz, B Schwalb, A Kiesel, C Baejen, P Torkler, J Gagneur, J Soeding, ...
Cell 155 (5), 1075-1087, 2013
Mandates: German Research Foundation
WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs
C Galiez, M Siebert, F Enault, J Vincent, J Söding
Bioinformatics 33 (19), 3113-3114, 2017
Mandates: European Commission
A vocabulary of ancient peptides at the origin of folded proteins
V Alva, J Söding, AN Lupas
elife 4, e09410, 2015
Mandates: Howard Hughes Medical Institute
The Mre11: Rad50 structure shows an ATP-dependent molecular clamp in DNA double-strand break repair
K Lammens, DJ Bemeleit, C Möckel, E Clausing, A Schele, S Hartung, ...
Cell 145 (1), 54-66, 2011
Mandates: US National Institutes of Health, German Research Foundation
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets
M Hauser, M Steinegger, J Söding
Bioinformatics 32 (9), 1323-1330, 2016
Mandates: German Research Foundation
Foldseek: fast and accurate protein structure search
M van Kempen, SS Kim, C Tumescheit, M Mirdita, CLM Gilchrist, J Söding, ...
Biorxiv, 2022.02. 07.479398, 2022
Mandates: Federal Ministry of Education and Research, Germany
MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics
E Levy Karin, M Mirdita, J Söding
Microbiome 8, 1-15, 2020
Mandates: European Commission
RECQL5 controls transcript elongation and suppresses genome instability associated with transcription stress
M Saponaro, T Kantidakis, R Mitter, GP Kelly, M Heron, H Williams, ...
Cell 157 (5), 1037-1049, 2014
Mandates: Cancer Research UK, Worldwide Cancer Research, UK, European Commission
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