Laboratory for Computational Biology & Molecular Machine Learning

Team

We are hiring at all levels (interns, graduate students, postdocs, and research software engineers) excited for large-scale data processing, HPC/GPU programming, machine learning or open-source scientific software. Send a short introduction and CV to milot@mirdita.org.

Choonghwan Lee Intern

Dohyun Lim Intern

Hongju Lee Intern

Jaewon Kim Intern

Milot Mirdita Assistant Professor at SKKU

Seda Nur Kabadayi Intern

Yul Kim Intern

+ You? Join us

Publications

Full list available on ORCID or Google Scholar.

• Multiple protein structure alignment at scale with FoldMason

  Cameron L. M. Gilchrist, Milot Mirdita, and Martin Steinegger. Science (2026) · DOI ⧉

• Protein structure-informed bacteriophage genome annotation with Phold

  George Bouras et al. Nucleic Acids Research (2026) · DOI ⧉

• GPU-accelerated homology search with MMseqs2

  Felix Kallenborn, Alejandro Chacon, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt, and Martin Steinegger. Nature Methods (2025) · DOI ⧉

• De novo discovery of conserved gene clusters in microbial genomes with Spacedust

  Ruoshi Zhang, Milot Mirdita, and Johannes Söding. Nature Methods (2025) · DOI ⧉

• AlphaFold Protein Structure Database and 3D-Beacons: new data and capabilities

  Jennifer Fleming et al. Journal of Molecular Biology (2025) · DOI ⧉

• Rapid and sensitive protein complex alignment with Foldseek-Multimer

  Woosub Kim, Milot Mirdita, Eli Levy Karin, Cameron L. M. Gilchrist, Hugo Schweke, Johannes Söding, Emmanuel D. Levy, and Martin Steinegger. Nature Methods (2025) · DOI ⧉

• Easy and accurate protein structure prediction using ColabFold

  Gyuri Kim, Sewon Lee, Eli Levy Karin, Hyunbin Kim, Yoshitaka Moriwaki, Sergey Ovchinnikov, Martin Steinegger, and Milot Mirdita. Nature Protocols (2025) · DOI ⧉

• Easy and interactive taxonomic profiling with Metabuli App

  SunJae Lee, Jaebeom Kim, Milot Mirdita, Cameron L.M. Gilchrist, and Martin Steinegger. bioRxiv (2025) · DOI ⧉

• BFVD—a large repository of predicted viral protein structures

  Rachel Seongeun Kim, Eli Levy Karin, Milot Mirdita, Rayan Chikhi, and Martin Steinegger. Nucleic Acids Research (2025) · DOI ⧉

• Metagenomic-scale analysis of the predicted protein structure universe

  Jingi Yeo et al. bioRxiv (2025) · DOI ⧉

• Structural motif search across the protein-universe with Folddisco

  Hyunbin Kim, Rachel Seongeun Kim, Milot Mirdita, and Martin Steinegger. bioRxiv (2025) · DOI ⧉

• Scaling down protein language modeling with MSA Pairformer

  Yo Akiyama, Zhidian Zhang, Milot Mirdita, Martin Steinegger, and Sergey Ovchinnikov. bioRxiv (2025) · DOI ⧉

• Bilingual language model for protein sequence and structure

  Michael Heinzinger, Konstantin Weissenow, Joaquin Gomez Sanchez, Adrian Henkel, Milot Mirdita, Martin Steinegger, and Burkhard Rost. NAR Genomics and Bioinformatics (2024) · DOI ⧉

• Petabase-scale homology search for structure prediction

  Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, and Martin Steinegger. Cold Spring Harbor Perspectives in Biology (2024) · DOI ⧉

• Fast and accurate protein structure search with Foldseek

  Michel Van Kempen, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, Jeongjae Lee, Cameron L. M. Gilchrist, Johannes Söding, and Martin Steinegger. Nature Biotechnology (2024) · DOI ⧉

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

  Mihaly Varadi et al. Nucleic Acids Research (2024) · DOI ⧉

• DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options

  Sushmita Basu et al. Nucleic Acids Research (2024) · DOI ⧉

• TransAnnot—a fast transcriptome annotation pipeline

  Mariia Zelenskaia, Yazhini Arangasamy, Milot Mirdita, Johannes Söding, and Venket Raghavan. Bioinformatics Advances (2024) · DOI ⧉

• The OMG dataset: an open MetaGenomic corpus for mixed-modality genomic language modeling

  Andre Cornman, Jacob West-Roberts, Antonio Pedro Camargo, Simon Roux, Martin Beracochea, Milot Mirdita, Sergey Ovchinnikov, and Yunha Hwang. bioRxiv (2024) · DOI ⧉

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

  Inigo Barrio-Hernandez, Jingi Yeo, Jürgen Jänes, Milot Mirdita, Cameron L. M. Gilchrist, Tanita Wein, Mihaly Varadi, Sameer Velankar, Pedro Beltrao, and Martin Steinegger. Nature (2023) · DOI ⧉

• Cross-phyla protein annotation by structural prediction and alignment

  Fabian Ruperti, Nikolaos Papadopoulos, Jacob M. Musser, Milot Mirdita, Martin Steinegger, and Detlev Arendt. Genome Biology (2023) · DOI ⧉

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

  Hyunbin Kim, Milot Mirdita, and Martin Steinegger. Bioinformatics (2023) · DOI ⧉

• LambdaPP: fast and accessible protein‐specific phenotype predictions

  Tobias Olenyi et al. Protein Science (2023) · DOI ⧉

• ColabFold: making protein folding accessible to all

  Milot Mirdita, Konstantin Schütze, Yoshitaka Moriwaki, Lim Heo, Sergey Ovchinnikov, and Martin Steinegger. Nature Methods (2022) · DOI ⧉

• SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts

  Ruoshi Zhang, Milot Mirdita, Eli Levy Karin, Clovis Norroy, Clovis Galiez, and Johannes Söding. Bioinformatics (2021) · DOI ⧉

• Fast and sensitive taxonomic assignment to metagenomic contigs

  M Mirdita, M Steinegger, F Breitwieser, J Söding, and E Levy Karin. Bioinformatics (2021) · DOI ⧉

• PredictProtein - predicting protein structure and function for 29 years

  Michael Bernhofer et al. Nucleic Acids Research (2021) · DOI ⧉

• Going to extremes – a metagenomic journey into the dark matter of life

  Arnthór Aevarsson et al. FEMS Microbiology Letters (2021) · DOI ⧉

• DescribePROT: database of amino acid-level protein structure and function predictions

  Bi Zhao et al. Nucleic Acids Research (2021) · DOI ⧉

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

  Eli Levy Karin, Milot Mirdita, and Johannes Söding. Microbiome (2020) · DOI ⧉

• Protein sequence analysis using the MPI bioinformatics toolkit

  Felix Gabler, Seung‐Zin Nam, Sebastian Till, Milot Mirdita, Martin Steinegger, Johannes Söding, Andrei N. Lupas, and Vikram Alva. Current Protocols in Bioinformatics (2020) · DOI ⧉

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

  Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, and Johannes Söding. BMC Bioinformatics (2019) · DOI ⧉

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

  Milot Mirdita, Martin Steinegger, and Johannes Söding. Bioinformatics (2019) · DOI ⧉

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

  Martin Steinegger, Milot Mirdita, and Johannes Söding. Nature Methods (2019) · DOI ⧉

• An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

  Chen Keasar et al. Scientific Reports (2018) · DOI ⧉

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

  Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J. Martin, Johannes Söding, and Martin Steinegger. Nucleic Acids Research (2017) · DOI ⧉

• Cloud prediction of protein structure and function with PredictProtein for Debian

  László Kaján et al. Biomed Research International (2013) · DOI ⧉