Martin Steinegger

Research interests

Publications

• AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities

  Journal of Molecular Biology · 2025 · 10.1016/j.jmb.2025.168967

• Bilingual language model for protein sequence and structure

  NAR Genomics and Bioinformatics · 2024 · 10.1093/nargab/lqae150

• Fast and accurate protein structure search with Foldseek

  Nature Biotechnology · 2023 · https://doi.org/10.1038/s41587-023-01773-0

• AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

  Nucleic Acids Research · 2023 · https://doi.org/10.1093/nar/gkad1011

• Clustering predicted structures at the scale of the known protein universe

  Nature · 2023 · 10.1038/s41586-023-06510-w

• ColabFold: making protein folding accessible to all

  Nature Methods · 2022 · https://doi.org/10.1038/s41592-022-01488-1

• Metagenome analysis using the Kraken software suite

  Nature Protocols · 2022 · https://doi.org/10.1038/s41596-022-00738-y

• ProtTrans: Toward Understanding the Language of Life Through Self-Supervised Learning

  IEEE Transactions on Pattern Analysis and Machine Intelligence · 2021 · https://doi.org/10.1109/tpami.2021.3095381

• ColabFold - Making protein folding accessible to all

  bioRxiv (Cold Spring Harbor Laboratory) · 2021 · 10.1101/2021.08.15.456425

• ColabFold - Making protein folding accessible to all

  bioRxiv (Cold Spring Harbor Laboratory) · 2021 · 10.5281/zenodo.5123297

• Applying and improving AlphaFold at CASP14

  Proteins Structure Function and Bioinformatics · 2021 · 10.1002/prot.26257

• Fast and sensitive taxonomic assignment to metagenomic contigs

  Bioinformatics · 2021 · 10.1093/bioinformatics/btab184

• PredictProtein - Predicting Protein Structure and Function for 29 Years

  Nucleic Acids Research · 2021 · 10.1093/nar/gkab354

• Highly accurate protein structure prediction with AlphaFold

  Nature · 2021 · https://doi.org/10.1038/s41586-021-03819-2

• Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank

  Genome biology · 2020 · 10.1186/s13059-020-02023-1

• ProtTrans: Towards Cracking the Language of Life’s Code Through Self-Supervised Learning

  bioRxiv (Cold Spring Harbor Laboratory) · 2020 · 10.1101/2020.07.12.199554

• Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

  Current Protocols in Bioinformatics · 2020 · 10.1002/cpbi.108

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

  BMC Bioinformatics · 2019 · 10.1186/s12859-019-3019-7

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

  Nature Methods · 2019 · 10.1038/s41592-019-0437-4

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

  Bioinformatics · 2019 · 10.1093/bioinformatics/bty1057

• Clustering huge protein sequence sets in linear time

  Nature Communications · 2018 · 10.1038/s41467-018-04964-5

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

  Nature Biotechnology · 2017 · https://doi.org/10.1038/nbt.3988

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

  Nucleic Acids Research · 2016 · 10.1093/nar/gkw1081

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

  Bioinformatics · 2016 · 10.1093/bioinformatics/btw006

Current projects

No projects listed.