Steinegger, Martin

Highly accurate protein structure prediction with AlphaFold

Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 43,764

ColabFold - Making protein folding accessible to all

Mirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S., & Steinegger, M. (2021) · Nature Methods

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 9,391

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

Steinegger, M., & Söding, J. (2017) · Nature Biotechnology

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 4,840

Fast and accurate protein structure search with Foldseek

van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2022) · Nature Biotechnology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2,598

Fast and accurate protein structure search with Foldseek

van Kempen, M., Kim, S. S., Tumescheit, C., Mirdita, M., Lee, J., Gilchrist, C. L. M., Söding, J., & Steinegger, M. (2024) · Nature Biotechnology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2,596

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

Elnaggar, A., Heinzinger, M., Dallago, C., Rehawi, G., Wang, Y., Jones, L., Gibbs, T., Feher, T., Angerer, C., Steinegger, M., et al. (2022) · IEEE Transactions on Pattern Analysis and Machine Intelligence

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 2,329

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

Varadi, M., Bertoni, D., Magana, P., Paramval, U., Pidruchna, I., Radhakrishnan, M., Tsenkov, M., Nair, S., Mirdita, M., Yeo, J., et al. (2024) · Nucleic Acids Research

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2,052

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

Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J., & Söding, J. (2019) · BMC Bioinformatics

Genomics and Phylogenetic StudiesProtein Structure and Dynamics

Cited by 1,145

Clustering huge protein sequence sets in linear time

Steinegger, M., & Söding, J. (2018) · Nature Communications

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 875

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit

Gabler, F., Nam, S., Till, S., Mirdita, M., Steinegger, M., Söding, J., Lupas, A. N., & Alva, V. (2020) · Current Protocols in Bioinformatics

Genomics and Phylogenetic StudiesProtein Structure and Dynamics

Cited by 831

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

Mirdita, M., Steinegger, M., & Söding, J. (2019) · Bioinformatics

Genomics and Phylogenetic StudiesAlgorithms and Data Compression

Cited by 618

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

Steinegger, M., Mirdita, M., & Söding, J. (2019) · Nature Methods

Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity Studies

Cited by 445

Clustering predicted structures at the scale of the known protein universe

Barrio-Hernandez, I., Yeo, J., Jänes, J., Mirdita, M., Gilchrist, C. L. M., Wein, T., Varadi, M., Velankar, S., Beltrao, P., & Steinegger, M. (2023) · Nature

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 362

Clustering predicted structures at the scale of the known protein universe

Steinegger, M., Beltrao, P., Velankar, S., Varadi, M., Wein, T., Gilchrist, C., Mirdita, M., Jänes, J., Yeo, J., & Barrio-Hernandez, I. (2023) · Nature

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 362

Clustering predicted structures at the scale of the known protein universe

Barrio-Hernandez, I., Yeo, J., Jänes, J., Wein, T., Varadi, M., Velankar, S., Beltrao, P., & Steinegger, M. (2023) · Nature

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 362

Bilingual Language Model for Protein Sequence and Structure

Heinzinger, M., Weissenow, K., Sanchez, J. G., Henkel, A., Mirdita, M., Steinegger, M., & Rost, B. (2023) · NAR Genomics and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 312

Bilingual language model for protein sequence and structure

Heinzinger, M., Weissenow, K., Sanchez, J. G., Henkel, A., Mirdita, M., Steinegger, M., & Rost, B. (2024) · NAR Genomics and Bioinformatics

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 311

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

Steinegger, M., & Salzberg, S. L. (2020) · Genome Biology

Genomics and Phylogenetic StudiesFractal and DNA sequence analysis

Cited by 246

Unifying the known and unknown microbial coding sequence space

Vanni, C., Schechter, M. S., Acinas, S. G., Barberán, A., Buttigieg, P. L., Casamayor, E. O., Delmont, T. O., Duarte, C. M., Eren, A. M., Finn, R. D., et al. (2022) · eLife

Genomics and Phylogenetic StudiesMicrobial Community Ecology and Physiology

Cited by 134

Multiple Protein Structure Alignment at Scale with FoldMason

Gilchrist, C. L. M., Mirdita, M., & Steinegger, M. (2024) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 117

Multiple protein structure alignment at scale with FoldMason

Gilchrist, C. L. M., Mirdita, M., & Steinegger, M. (2026) · Science

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 117

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Bordin, N., Sillitoe, I., Nallapareddy, V., Rauer, C., Lam, S. D., Waman, V. P., Sen, N., Heinzinger, M., Littmann, M., Kim, S., et al. (2022) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 103

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Bordin, N., Sillitoe, I., Nallapareddy, V., Rauer, C., Lam, S. D., Waman, V. P., Sen, N., Heinzinger, M., Littmann, M., Kim, S., et al. (2023) · Communications Biology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 103

BFVD—a large repository of predicted viral protein structures

Kim, R. S., Levy Karin, E., Mirdita, M., Chikhi, R., & Steinegger, M. (2025) · Nucleic Acids Research

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 86