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This interview with Martin Steinegger discusses his contributions to bioinformatics, including the development of MMseqs2, Foldseek, and ColabFold, which have significantly advanced protein sequence and structure analysis. Steinegger reflects on his academic path, the development of these tools, and the broader implications for computational biology. The interview highlights the importance of user-friendly, open-source methods in accelerating biological research, as exemplified by his work enabling large-scale protein structure searches and accessible structure prediction.
Meet the bioinformatician who isn't from DeepMind but helped revolutionize protein structure prediction with tools like MMseqs2 and Foldseek.
Abstract In the 2021 Nature paper [1] that introduced the groundbreaking protein structure prediction artificial intelligent (AI) tool AlphaFold2 to the world, Martin Steinegger was the only author who was not affiliated with DeepMind. At the forefront of the ongoing revolution in biological research methodology, Steinegger has pioneered the development of a series of powerful bioinformatics tools, including MMseqs2 [2] for protein and nucleotide sequence searching and clustering, Foldseek [3] for protein structure searches at the scale of the AlphaFold database and ColabFold [4] for rapid and accessible protein structure prediction. After earning his PhD in Computer Science with summa cum laude honors from the Technical University of Munich in 2018, based on his doctoral research that was conducted at the Max Planck Institute for Multidisciplinary Sciences, Steinegger completed a postdoctoral fellowship at Johns Hopkins University. He is now an associate professor in the Biology Department at Seoul National University in the Republic of Korea, with a joint appointment to the Interdisciplinary Program in Bioinformatics. His group develops user-friendly, open-source methods for protein sequence and structure analysis. In recognition of his scientific contributions, Steinegger received the prestigious 2024 Overton Award from the International Society for Computational Biology. In this interview with NSR, Steinegger shares his unconventional academic journey, his experiences in developing these transformative tools and his insights into the rapidly evolving field of computational biology.
