| ColabFold - Making protein folding accessible to all M Mirdita, K Schütze, Y Moriwaki, L Heo, S Ovchinnikov, M Steinegger Nature Methods 19, 679–682, 2022 | 9039 | 2022 |
| Fast and accurate protein structure search with Foldseek M van Kempen, SS Kim, C Tumescheit, M Mirdita, Lee, ... Nature Biotechnology 42, 243–246, 2023 | 2354* | 2023 |
| AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences M Varadi, D Bertoni, P Magana, U Paramval, I Pidruchna, ... Nucleic Acids Research 52 (D1), D368-D375, 2024 | 1712 | 2024 |
| HH-suite3 for fast remote homology detection and deep protein annotation M Steinegger, M Meier, M Mirdita, H Voehringer, SJ Haunsberger, ... BMC Bioinformatics 20 (1), 473, 2019 | 1249 | 2019 |
| 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 | 839 | 2020 |
| Uniclust databases of clustered and deeply annotated protein sequences and alignments M Mirdita, L von den Driesch, C Galiez, MJ Martin, J Söding, M Steinegger Nucleic Acids Research 45 (D1), D170-D176, 2017 | 834 | 2017 |
| MMseqs2 desktop and local web server app for fast, interactive sequence searches M Mirdita, M Steinegger, J Söding Bioinformatics 35 (16), 2856-2858, 2019 | 605 | 2019 |
| Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold M Steinegger, M Mirdita, J Söding Nature Methods 16 (7), 603-606, 2019 | 507 | 2019 |
| Clustering predicted structures at the scale of the known protein universe I Barrio-Hernandez, J Yeo, J Jänes, M Mirdita, CLM Gilchrist, T Wein, ... Nature 622, 637–645, 2023 | 350 | 2023 |
| Bilingual language model for protein sequence and structure M Heinzinger, K Weissenow, JG Sanchez, A Henkel, M Mirdita, ... NAR Genomics and Bioinformatics 6 (4), lqae150, 2024 | 309 | 2024 |
| PredictProtein - Predicting Protein Structure and Function for 29 Years M Bernhofer, C Dallago, T Karl, V Satagopam, M Heinzinger, M Littmann, ... Nucleic Acids Research 49 (W1), W535–W540, 2021 | 294 | 2021 |
| MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics E Levy Karin, M Mirdita, J Söding Microbiome 8 (1), 48, 2020 | 292 | 2020 |
| Fast and sensitive taxonomic assignment to metagenomic contigs M Mirdita, M Steinegger, F Breitwieser, J Soeding, E Levy Karin Bioinformatics 37 (18), 3029–3031, 2021 | 273 | 2021 |
| Easy and accurate protein structure prediction using ColabFold G Kim, S Lee, E Levy Karin, H Kim, Y Moriwaki, S Ovchinnikov, ... Nature Protocols 20, 620–642, 2024 | 118 | 2024 |
| SpacePHARER: Sensitive identification of phages from CRISPR spacers in prokaryotic hosts R Zhang, M Mirdita, E Levy Karin, C Norroy, C Galiez, J Soeding Bioinformatics 37 (19), 3364–3366, 2021 | 103 | 2021 |
| DescribePROT: database of amino acid-level protein structure and function predictions B Zhao, A Katuwawala, CJ Oldfield, AK Dunker, E Faraggi, J Gsponer, ... Nucleic Acids Research 49 (D1), D298-D308, 2021 | 75 | 2021 |
| Multiple protein structure alignment at scale with FoldMason CLM Gilchrist, M Mirdita, M Steinegger bioRxiv, 2024.08.01.606130, 2024 | 74 | 2024 |
| BFVD—a large repository of predicted viral protein structures RS Kim, E Levy Karin, M Mirdita, R Chikhi, M Steinegger Nucleic Acids Research 53 (D1), D340-D347, 2025 | 63 | 2025 |
| AlphaFold Protein Structure Database and 3D-Beacons: New Data and Capabilities J Fleming, P Magana, S Nair, M Tsenkov, D Bertoni, I Pidruchna, ... Journal of Molecular Biology, 168967, 2025 | 60 | 2025 |
| Rapid and sensitive protein complex alignment with Foldseek-Multimer W Kim, M Mirdita, E Levy Karin, CLM Gilchrist, H Schweke, J Söding, ... Nature Methods 22, 469-472, 2025 | 57 | 2025 |
Martin SteineggerAssociate Professor, Seoul National University, KoreaVerified email at snu.ac.kr
