Mirdita, Milot

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

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

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

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

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

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics

Levy Karin, E., Mirdita, M., & Söding, J. (2020) · Microbiome

Genomics and Phylogenetic StudiesEnvironmental DNA in Biodiversity Studies

Cited by 299

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

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

GPU-accelerated homology search with MMseqs2

Kallenborn, F., Chacon, A., Hundt, C., Sirelkhatim, H., Didi, K., Cha, S., Dallago, C., Mirdita, M., Schmidt, B., & Steinegger, M. (2024) · Nature Methods

Protein Structure and DynamicsParallel Computing and Optimization Techniques

Cited by 72

Protein Structure Informed Bacteriophage Genome Annotation with Phold

Bouras, G., Grigson, S. R., Mirdita, M., Heinzinger, M., Papudeshi, B., Mallawaarachchi, V., Green, R., Kim, R. S., Mihalia, V., Psaltis, A. J., et al. (2025) · Nucleic Acids Research

Bacteriophages and microbial interactionsGenomics and Phylogenetic Studies

Cited by 71

Protein structure-informed bacteriophage genome annotation with Phold

Bouras, G., Grigson, S. R., Mirdita, M., Heinzinger, M., Papudeshi, B., Mallawaarachchi, V., Green, R., Kim, R. S., Mihalia, V., Psaltis, A. J., et al. (2026) · Nucleic Acids Research

Bacteriophages and microbial interactionsGenomics and Phylogenetic Studies

Cited by 71

Cross-phyla protein annotation by structural prediction and alignment

Ruperti, F., Papadopoulos, N., Musser, J. M., Mirdita, M., Steinegger, M., & Arendt, D. (2023) · Genome Biology

Genomics and Phylogenetic StudiesProtein Structure and Dynamics

Cited by 38

Democratizing protein language model training, sharing and collaboration

Su, J., Li, Z., Tao, T., Han, C., He, Y., Dai, F., Yuan, Q., Gao, Y., Si, T., Zhang, X., et al. (2026) · Nature Biotechnology

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 35

Foldcomp: a library and format for compressing and indexing large protein structure sets

Kim, H., Mirdita, M., & Steinegger, M. (2023) · Bioinformatics

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 29

LambdaPP: Fast and accessible protein-specific phenotype predictions

Olenyi, T., Marquet, C., Heinzinger, M., Kröger, B., Nikolova, T., Bernhofer, M., Sändig, P., Schütze, K., Littmann, M., Mirdita, M., et al. (2022) · Protein Science

Machine Learning in BioinformaticsProtein Structure and Dynamics

Cited by 18

Structural motif search across the protein universe with Folddisco

Kim, H., Kim, R. S., Mirdita, M., Yoon, J., & Steinegger, M. (2026) · Nature Biotechnology

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 10