Publications

De novo discovery of conserved gene clusters in microbial genomes with Spacedust
Metagenomics has revolutionized environmental and human-associated microbiome studies. However, the limited fraction of proteins with …
Ruoshi Zhang, Milot Mirdita, Johannes Söding
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GPU-accelerated homology search with MMseqs2
Rapidly growing protein databases demand faster sensitive search tools. Here the graphics processing unit (GPU)-accelerated MMseqs2 …
Felix Kallenborn, Alejandro Chacon, Christian Hundt, Hassan Sirelkhatim, Kieran Didi, Sooyoung Cha, Christian Dallago, Milot Mirdita, Bertil Schmidt, Martin Steinegger
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AlphaFold Protein Structure Database and 3D-Beacons: new data and capabilities
The AlphaFold Protein Structure Database (https://alphafold.ebi.ac.uk/) has made significant strides in enhancing its utility and …
Jennifer Fleming, Paulyna Magana, Sreenath Nair, Maxim Tsenkov, Damian Bertoni, Ivanna Pidruchna, Marcelo Querino Lima Afonso, Adam Midlik, Urmila Paramval, Augustin Žídek, Agata Laydon, Oleg Kovalevskiy, Joshua Pan, Jun Cheng, Žiga Avsec, Clare Bycroft, Lai Hong Wong, Meera Last, Milot Mirdita, Martin Steinegger, Pushmeet Kohli, Mihaly Varadi, Sameer Velankar
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Rapid and sensitive protein complex alignment with Foldseek-Multimer
Advances in computational structure prediction will vastly augment the hundreds of thousands of currently available protein complex …
Woosub Kim, Milot Mirdita, Eli Levy Karin, Cameron L. M. Gilchrist, Hugo Schweke, Johannes Söding, Emmanuel D. Levy, Martin Steinegger
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Easy and interactive taxonomic profiling with Metabuli App
Accurate metagenomic taxonomic profiling is critical for understanding microbial communities. However, computational analysis often …
SunJae Lee, Jaebeom Kim, Milot Mirdita, Cameron L.M. Gilchrist, Martin Steinegger
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Easy and accurate protein structure prediction using ColabFold
Since its public release in 2021, AlphaFold2 (AF2) has made investigating biological questions, by using predicted protein structures …
Gyuri Kim, Sewon Lee, Eli Levy Karin, Hyunbin Kim, Yoshitaka Moriwaki, Sergey Ovchinnikov, Martin Steinegger, Milot Mirdita
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Structural motif search across the protein-universe with Folddisco
Detecting similar protein structural motifs, functionally crucial short 3D patterns, in large structure collections is computationally …
Hyunbin Kim, Rachel Seongeun Kim, Milot Mirdita, Martin Steinegger
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Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast …
Yo Akiyama, Zhidian Zhang, Milot Mirdita, Martin Steinegger, Sergey Ovchinnikov
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Protein structure informed bacteriophage genome annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as …
George Bouras, Susanna R Grigson, Milot Mirdita, Michael Heinzinger, Bhavya Papudeshi, Vijini Mallawaarachchi, Renee Green, Rachel Seongeun Kim, Victor Mihalia, Alkis James Psaltis, Others
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Metagenomic-scale analysis of the predicted protein structure universe
Protein structure prediction breakthroughs, notably AlphaFold2 and ESMfold, have led to an unprecedented influx of computationally …
Jingi Yeo, Yewon Han, Nicola Bordin, Andy M Lau, Shaun Mathew Kandathil, Hyunbin Kim, Eli Levy Karin, Milot Mirdita, David Tudor Jones, Christine Orengo, Others
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Highly efficient protein structure prediction on NVIDIA RTX Blackwell and Grace-Hopper
Kieran Didi, Prashant Sohani, Fabian Berressem, Alexander Nesterovskiy, Boris Fomitchev, Robert Ohannessian, Mohamed Elbalkini, Jonathan Cogan, Anthony Costa, Arash Vahdat, Others
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BFVD—a large repository of predicted viral protein structures
The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. …
Rachel Seongeun Kim, Eli Levy Karin, Milot Mirdita, Rayan Chikhi, Martin Steinegger
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Bilingual language model for protein sequence and structure
Adapting language models to protein sequences spawned the development of powerful protein language models (pLMs). Concurrently, …
Michael Heinzinger, Konstantin Weissenow, Joaquin Gomez Sanchez, Adrian Henkel, Milot Mirdita, Martin Steinegger, Burkhard Rost
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Petabase-scale homology search for structure prediction
The recent CASP15 competition highlighted the critical role of multiple sequence alignments (MSAs) in protein structure prediction, as …
Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, Martin Steinegger
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Fast and accurate protein structure search with Foldseek
As structure prediction methods are generating millions of publicly available protein structures, searching these databases is becoming …
Michel Van Kempen, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, Jeongjae Lee, Cameron L. M. Gilchrist, Johannes Söding, Martin Steinegger
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TransAnnot—a fast transcriptome annotation pipeline
The annotation of deeply sequenced, de novo assembled transcriptomes continues to be a challenge as some of the state-of-the-art tools …
Mariia Zelenskaia, Yazhini Arangasamy, Milot Mirdita, Johannes Söding, Venket Raghavan
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The OMG dataset: an open MetaGenomic corpus for mixed-modality genomic language modeling
Biological language model performance depends heavily on pretraining data quality, diversity, and size. While metagenomic datasets …
Andre Cornman, Jacob West-Roberts, Antonio Pedro Camargo, Simon Roux, Martin Beracochea, Milot Mirdita, Sergey Ovchinnikov, Yunha Hwang
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Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related …
Cameron LM Gilchrist, Milot Mirdita, Martin Steinegger
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DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options
The DescribePROT database of amino acid-level descriptors of protein structures and functions was substantially expanded since its …
Sushmita Basu, Bi Zhao, Bálint Biró, Eshel Faraggi, Jörg Gsponer, Gang Hu, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Johannes Söding, Martin Steinegger, Duolin Wang, Kui Wang, Dong Xu, Jian Zhang, Lukasz Kurgan
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AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences
The AlphaFold Database Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) has significantly impacted structural …
Mihaly Varadi, Damian Bertoni, Paulyna Magana, Urmila Paramval, Ivanna Pidruchna, Malarvizhi Radhakrishnan, Maxim Tsenkov, Sreenath Nair, Milot Mirdita, Jingi Yeo, Oleg Kovalevskiy, Kathryn Tunyasuvunakool, Agata Laydon, Augustin Žídek, Hamish Tomlinson, Dhavanthi Hariharan, Josh Abrahamson, Tim Green, John Jumper, Ewan Birney, Martin Steinegger, Demis Hassabis, Sameer Velankar
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Clustering predicted structures at the scale of the known protein universe
Proteins are key to all cellular processes and their structure is important in understanding their function and evolution. …
Inigo Barrio-Hernandez, Jingi Yeo, Jürgen Jänes, Milot Mirdita, Cameron L. M. Gilchrist, Tanita Wein, Mihaly Varadi, Sameer Velankar, Pedro Beltrao, Martin Steinegger
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Cross-phyla protein annotation by structural prediction and alignment
Background Protein annotation is a major goal in molecular biology, yet experimentally determined knowledge is typically limited to a …
Fabian Ruperti, Nikolaos Papadopoulos, Jacob M. Musser, Milot Mirdita, Martin Steinegger, Detlev Arendt
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Foldcomp: a library and format for compressing and indexing large protein structure sets
Highly accurate protein structure predictors have generated hundreds of millions of protein structures; these pose a challenge in terms …
Hyunbin Kim, Milot Mirdita, Martin Steinegger
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LambdaPP: fast and accessible protein‐specific phenotype predictions
The availability of accurate and fast artificial intelligence (AI) solutions predicting aspects of proteins are revolutionizing …
Tobias Olenyi, Céline Marquet, Michael Heinzinger, Benjamin Kröger, Tiha Nikolova, Michael Bernhofer, Philip Sändig, Konstantin Schütze, Maria Littmann, Milot Mirdita, Martin Steinegger, Christian Dallago, Burkhard Rost
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ColabFold: making protein folding accessible to all
ColabFold offers accelerated prediction of protein structures and complexes by combining the fast homology search of MMseqs2 with …
Milot Mirdita, Konstantin Schütze, Yoshitaka Moriwaki, Lim Heo, Sergey Ovchinnikov, Martin Steinegger
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SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts
SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via …
Ruoshi Zhang, Milot Mirdita, Eli Levy Karin, Clovis Norroy, Clovis Galiez, Johannes Söding
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Fast and sensitive taxonomic assignment to metagenomic contigs
MMseqs2 taxonomy is a new tool to assign taxonomic labels to metagenomic contigs. It extracts all possible protein fragments from each …
M Mirdita, M Steinegger, F Breitwieser, J Söding, E Levy Karin
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PredictProtein - predicting protein structure and function for 29 years
Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site …
Michael Bernhofer, Christian Dallago, Tim Karl, Venkata Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, Laszlo Kajan, Sean O’Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost
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Going to extremes – a metagenomic journey into the dark matter of life
The Virus-X—Viral Metagenomics for Innovation Value—project was a scientific expedition to explore and exploit uncharted territory of …
Arnthór Aevarsson, Anna-Karina Kaczorowska, Björn Thor Adalsteinsson, Josefin Ahlqvist, Salam Al-Karadaghi, Joseph Altenbuchner, Hasan Arsin, Úlfur Áugúst Átlasson, David Brandt, Magdalena Cichowicz-Cieślak, Katy A S Cornish, Jérémy Courtin, Slawomir Dabrowski, Håkon Dahle, Samia Djeffane, Sebastian Dorawa, Julia Dusaucy, Francois Enault, Anita-Elin Fedøy, Stefanie Freitag-Pohl, Olafur H Fridjonsson, Clovis Galiez, Eirin Glomsaker, Mickael Guérin, Sigurd E Gundesø, Elisabet E Gudmundsdóttir, Hördur Gudmundsson, Maria Håkansson, Christian Henke, Alexandra Helleux, Jørn Remi Henriksen, Sigrídur Hjörleifdóttir, Gudmundur O Hreggvidsson, Andrius Jasilionis, Annika Jochheim, Ilmur Jónsdóttir, Lilja Björk Jónsdóttir, Agata Jurczak-Kurek, Tadeusz Kaczorowski, Jörn Kalinowski, Lukasz P Kozlowski, Mart Krupovic, Karolina Kwiatkowska-Semrau, Olav Lanes, Joanna Lange, Julien Lebrat, Javier Linares-Pastén, Ying Liu, Steffen A Lorentsen, Tobias Lutterman, Thibaud Mas, William Merré, Milot Mirdita, Agnieszka Morzywołek, Eric Olo Ndela, Eva Nordberg Karlsson, Edda Olgudóttir, Cathrine Pedersen, Francine Perler, Sólveig K Pétursdóttir, Magdalena Plotka, Ehmke Pohl, David Prangishvili, Jessica L Ray, Birkir Reynisson, Tara Róbertsdóttir, Ruth-Anne Sandaa, Alexander Sczyrba, Sigurlaug Skírnisdóttir, Johannes Söding, Terese Solstad, Ida H Steen, Sigmar Karl Stefánsson, Martin Steinegger, Katrine Stange Overå, Bernd Striberny, Anders Svensson, Monika Szadkowska, Emma J Tarrant, Paul Terzian, Mathilde Tourigny, Tom van den Bergh, Justine Vanhalst, Jonathan Vincent, Bas Vroling, Björn Walse, Lei Wang, Hildegard Watzlawick, Martin Welin, Olesia Werbowy, Ewa Wons, Ruoshi Zhang
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DescribePROT: database of amino acid-level protein structure and function predictions
We present DescribePROT, the database of predicted amino acid-level descriptors of structure and function of proteins. DescribePROT …
Bi Zhao, Akila Katuwawala, Christopher J Oldfield, A Keith Dunker, Eshel Faraggi, Jörg Gsponer, Andrzej Kloczkowski, Nawar Malhis, Milot Mirdita, Zoran Obradovic, Johannes Söding, Martin Steinegger, Yaoqi Zhou, Lukasz Kurgan
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Protein sequence analysis using the MPI bioinformatics toolkit
The MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) provides interactive access to a wide range of the best‐performing …
Felix Gabler, Seung‐Zin Nam, Sebastian Till, Milot Mirdita, Martin Steinegger, Johannes Söding, Andrei N. Lupas, Vikram Alva
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MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics
Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, …
Eli Levy Karin, Milot Mirdita, Johannes Söding
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HH-suite3 for fast remote homology detection and deep protein annotation
HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is …
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding
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MMseqs2 desktop and local web server app for fast, interactive sequence searches
The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases …
Milot Mirdita, Martin Steinegger, Johannes Söding
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Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold
The open-source de novo protein-level assembler, Plass (https://plass.mmseqs.com), assembles six-frame-translated sequencing reads into …
Martin Steinegger, Milot Mirdita, Johannes Söding
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly …
Chen Keasar, Liam J. McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B. K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergey Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena Ślusarz, Rafal Ślusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Foldit Players consortium, Ahmet Caglar, Alan Coral, Alison MacMillan, Allen Lubow, Barbara Failer, Bruno Kestemont, Catherine R. Landers, Charles Robert Painter, Christophe Garnier, Claudine Sellin, Dietmar Janz, Douglas Craig Wheeler, Vera Simon, Dylan M. Flear, Emmanuel Croze, George Victor McIlvaine, Gil Beecher, Gordon Lawrie, Guy Ykman, Harald Feldmann, Heidemarie K. Fuentes, Hosokawa Terumasa, Istvan Kovanecz, James Absalom Longino, Jan Hendrik Nijland, Jasper A. Diderich, Jeffrey M. Canfield, Jesper Eriksson, Jesse David Slone, Joan Goldsworthy Appel, Joanne Mitchell, John Mitch, Jorn Loots-Boiy, June M. Brownlee, Karsten Wilson, Keith T. Clayton, Kenneth E. DeFord, Kirk J. Abbey, Larry Withers, Linda Wei, Lloyd Ives, Lori A. Miller, Lynn Carpenter, Manasa G. Sharma, Manuel Ricci, Mark Stewart Binfield, Matthew John Davids, Matthias Gaebel, Michael D. Cassidy, Michael Fagiola, Michael Pfützenreuter, Nova Barlow, Peter John Triggiani, Renton Braden Mathew Innes, Robert Leduc, Rodrigo Luccas Corrêa Dos Santos Gomes, Rosemarie L. R. Morneau, Scott J. Zaccanelli, Susan C. Kleinfelter, T. J. A. Van Der Laan, Thomas Bausewein, Thomas J. George, Varichev Mikhail, Walter Barmettler, Silvia N. Crivelli
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Uniclust databases of clustered and deeply annotated protein sequences and alignments
We present three clustered protein sequence databases, Uniclust90, Uniclust50, Uniclust30 and three databases of multiple sequence …
Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J. Martin, Johannes Söding, Martin Steinegger
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Cloud prediction of protein structure and function with PredictProtein for Debian
We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. …
Laszlo Kajan, Guy Yachdav, Esmeralda Vicedo, Martin Steinegger, Milot Mirdita, Christof Angermüller, Ariane Böhm, Simon Domke, Julia Ertl, Christian Mertes, Eva Reisinger, Cedric Staniewski, Burkhard Rost
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