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

Nature biotechnology, 2017-11, Vol.35 (11), p.1026-1028

2017

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

Nature methods, 2012-02, Vol.9 (2), p.173-175

2012

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Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

Cell, 2013-11, Vol.155 (5), p.1075-1087

2013

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Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families

PLoS computational biology, 2021-04, Vol.17 (4), p.e1008798-e1008798

2021

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Transcriptome maps of general eukaryotic RNA degradation factors

eLife, 2019-05, Vol.8

2019

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A structural model of the active ribosome-bound membrane protein insertase YidC

eLife, 2014-07, Vol.3, p.e03035-e03035

2014

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Reconstructing complex lineage trees from scRNA-seq data using MERLoT

Nucleic acids research, 2019-09, Vol.47 (17), p.8961-8974

2019

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Clustering huge protein sequence sets in linear time

Nature communications, 2018-06, Vol.9 (1), p.2542-8, Article 2542

2018

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Large‐scale analysis of Drosophila core promoter function using synthetic promoters

Molecular systems biology, 2022-02, Vol.18 (2), p.e9816-n/a

2022

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

Bioinformatics (Oxford, England), 2014-11, Vol.30 (21), p.3128-3130

2014

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

Bioinformatics (Oxford, England), 2019-08, Vol.35 (16), p.2856-2858

2019

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

Nature methods, 2019-07, Vol.16 (7), p.603-606

2019

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

Nucleic acids research, 2016-07, Vol.44 (13), p.6055

2016

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Fast and accurate protein structure search with Foldseek

Nature biotechnology, 2024-02, Vol.42 (2), p.243-246

2024

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

BMC bioinformatics, 2019-09, Vol.20 (1), p.473-473, Article 473

2019

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Big-data approaches to protein structure prediction

Science (American Association for the Advancement of Science), 2017-01, Vol.355 (6322), p.248-249

Soding, Johannes

2017

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Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

Bioinformatics, 2021-07, Vol.37 (Supplement_1), p.i308-i316

2021

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

Journal of molecular biology, 2018-07, Vol.430 (15), p.2237-2243

2018

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Fast and accurate automatic structure prediction with HHpred

Proteins, structure, function, and bioinformatics, 2009, Vol.77 (S9), p.128-132

2009

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

Bioinformatics, 2016-05, Vol.32 (9), p.1323-1330

2016

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

PLoS computational biology, 2015-10, Vol.11 (10), p.e1004343-e1004343

2015

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Mechanisms for Active Regulation of Biomolecular Condensates

Trends in cell biology, 2020-01, Vol.30 (1), p.4-14

2020

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

Nucleic acids research, 2016-07, Vol.44 (W1), p.W410-W415

2016

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

Bioinformatics (Oxford, England), 2017-10, Vol.33 (19), p.3113-3114

2017

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Uniclust databases of clustered and deeply annotated protein sequences and alignments

Nucleic acids research, 2017-01, Vol.45 (D1), p.D170-D176

2017

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

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

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families

Transcriptome maps of general eukaryotic RNA degradation factors

A structural model of the active ribosome-bound membrane protein insertase YidC

Reconstructing complex lineage trees from scRNA-seq data using MERLoT

Clustering huge protein sequence sets in linear time

Large‐scale analysis of Drosophila core promoter function using synthetic promoters

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

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

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

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

Fast and accurate protein structure search with Foldseek

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

Big-data approaches to protein structure prediction

Thermodynamic modeling reveals widespread multivalent binding by RNA-binding proteins

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

Fast and accurate automatic structure prediction with HHpred

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

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

Mechanisms for Active Regulation of Biomolecular Condensates

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

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

Uniclust databases of clustered and deeply annotated protein sequences and alignments

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