Publications

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 (2023). DescribePROT in 2023: more, higher-quality and experimental annotations and improved data download options. Nucleic Acids Research.

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 (2023). AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Research.

Inigo Barrio-Hernandez, Jingi Yeo, Jürgen Jänes, Milot Mirdita, Cameron L. M. Gilchrist, Tanita Wein, Mihaly Varadi, Sameer Velankar, Pedro Beltrao, Martin Steinegger (2023). Clustering predicted structures at the scale of the known protein universe. Nature.

Michel van Kempen, Stephanie S Kim, Charlotte Tumescheit, Milot Mirdita, Jeongjae Lee, Cameron L M Gilchrist, Johannes Söding, Martin Steinegger (2023). Fast and accurate protein structure search with Foldseek. Nature Biotechnology.

Fabian Ruperti, Nikolaos Papadopoulos, Jacob M. Musser, Milot Mirdita, Martin Steinegger, Detlev Arendt (2023). Cross-phyla protein annotation by structural prediction and alignment. Genome Biology.

Hyunbin Kim, Milot Mirdita, Martin Steinegger (2023). Foldcomp: a library and format for compressing and indexing large protein structure sets. Bioinformatics.

Sewon Lee, Gyuri Kim, Eli Levy Karin, Milot Mirdita, Sukhwan Park, Rayan Chikhi, Artem Babaian, Andriy Kryshtafovych, Martin Steinegger (2023). Petascale Homology Search for Structure Prediction. bioRxiv.

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 (2023). LambdaPP: Fast and accessible protein‐specific phenotype predictions. Protein Science.

Gyuri Kim, Sewon Lee, Eli Levy Karin, Hyunbin Kim, Yoshitaka Moriwaki, Sergey Ovchinnikov, Martin Steinegger, Milot Mirdita (2023). Easy and accurate protein structure prediction using ColabFold. Protocol Exchange.

Milot Mirdita, Konstantin Schütze, Yoshitaka Moriwaki, Lim Heo, Sergey Ovchinnikov, Martin Steinegger (2022). ColabFold: making protein folding accessible to all. Nature Methods.

Ruoshi Zhang, Milot Mirdita, Eli Levy Karin, Clovis Norroy, Clovis Galiez, Johannes Söding (2021). SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics.

Milot Mirdita, Martin Steinegger, Florian P Breitwieser, Johannes Söding, Eli Levy Karin (2021). Fast and sensitive taxonomic assignment to metagenomic contigs. Bioinformatics.

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 (2021). PredictProtein - Predicting Protein Structure and Function for 29 Years. Nucleic Acids Research.

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 Sk\ŕnisdóttir, 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 (2021). Going to extremes - a metagenomic journey into the dark matter of life.. FEMS microbiology letters.

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 (2021). DescribePROT: database of amino acid-level protein structure and function predictions. Nucleic Acids Research.

Felix Gabler, Seung‐Zin Nam, Sebastian Till, Milot Mirdita, Martin Steinegger, Johannes Söding, Andrei N. Lupas, Vikram Alva (2020). Protein Sequence Analysis Using the MPI Bioinformatics Toolkit. Current Protocols in Bioinformatics.

Eli Levy Karin, Milot Mirdita, Johannes Söding (2020). MetaEuk-sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics.. Microbiome.

Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer, Stephan J. Haunsberger, Johannes Söding (2019). HH-suite3 for fast remote homology detection and deep protein annotation.. BMC Bioinformatics.

Milot Mirdita, Martin Steinegger, Johannes Söding (2019). MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics.

Martin Steinegger, Milot Mirdita, Johannes Söding (2019). Protein-level assembly increases protein sequence recovery from metagenomic samples manyfold. Nature Methods.

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, 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 (2018). An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. Scientific Reports.

Milot Mirdita, Lars von den Driesch, Clovis Galiez, Maria J. Martin, Johannes Söding, Martin Steinegger (2017). Uniclust databases of clustered and deeply annotated protein sequences and alignments. Nucleic Acids Research.

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 (2013). Cloud Prediction of Protein Structure and Function with PredictProtein for Debian. BioMed Research International.