Steinegger, Martin

BFVD - a large repository of predicted viral protein structures

Kim, R. S., Karin, E. L., & Steinegger, M. (2024) · Nucleic Acids Research

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 86

Novel machine learning approaches revolutionize protein knowledge

Bordin, N., Dallago, C., Heinzinger, M., Kim, S., Littmann, M., Rauer, C., Steinegger, M., Rost, B., & Orengo, C. (2023) · Trends in Biochemical Sciences

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 72

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

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

Varabyou, A., Sommer, M. J., Erdogdu, B., Shinder, I., Minkin, I., Chao, K.-H., Park, S., Heinz, J., Pockrandt, C., Shumate, A., et al. (2023) · Genome Biology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 54

CHESS 3: an improved, comprehensive catalog of human genes and transcripts based on large-scale expression data, phylogenetic analysis, and protein structure

Varabyou, A., Sommer, M. J., Erdogdu, B., Shinder, I., Minkin, I., Chao, K.-H., Park, S., Heinz, J., Pockrandt, C., Shumate, A., et al. (2022) · Genome biology

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 54

Structure-guided isoform identification for the human transcriptome

Sommer, M. J., Cha, S., Varabyou, A., Rincon, N., Park, S., Minkin, I., Pertea, M., Steinegger, M., & Salzberg, S. L. (2022) · eLife

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 40

Highly accurate isoform identification for the human transcriptome

Sommer, M. J., Cha, S., Varabyou, A., Rincon, N., Park, S., Minkin, I., Pertea, M., Steinegger, M., & Salzberg, S. L. (2022) · eLife

Genomics and Phylogenetic StudiesRNA Research and Splicing

Cited by 40

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

3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., et al. (2022) · GigaScience

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 32

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

Discovery of highly active kynureninases for cancer immunotherapy through protein language model

Eom, H., Park, S., Cho, K. S., Lee, J., Kim, H., Kim, S., Yang, J., Han, Y.-H., Lee, J., Seok, C., et al. (2025) · Nucleic Acids Research

Enzyme Catalysis and ImmobilizationMachine Learning in Bioinformatics

Cited by 10

Discovery of Highly Active Kynureninases for Cancer Immunotherapy through Protein Language Model

Eom, H., Cho, K. S., Lee, J., Kim, S., Park, S., Kim, H., Yang, J., Han, Y.-H., Lee, J., Seok, C., et al. (2024) · Nucleic Acids Research

Enzyme Catalysis and ImmobilizationMachine Learning in Bioinformatics

Cited by 10

Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides

Hsiao, M.-H., Miao, Y., Liu, Z., Schütze, K., Limjunyawong, N., Chien, D. C.-C., Monteiro, W. D., Chu, L.-S., Morgenlander, W., Jayaraman, S., et al. (2024) · Molecular & Cellular Proteomics

Venomous Animal Envenomation and StudiesHealthcare and Venom Research

Cited by 6

Molecular Display of the Animal Meta-Venome for Discovery of Novel Therapeutic Peptides

Hsiao, M.-H., Miao, Y., Liu, Z., Schütze, K., Limjunyawong, N., Chien, D. C.-C., Monteiro, W. D., Chu, L.-S., Morgenlander, W., Jayaraman, S., et al. (2025) · Molecular & Cellular Proteomics

Venomous Animal Envenomation and StudiesHealthcare and Venom Research

Cited by 5

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Varadi, M., Nair, S., Sillitoe, I., Tauriello, G., Anyango, S., Bienert, S., Borges, C., Deshpande, M., Green, T., Hassabis, D., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 2