PRACE: A New Paradigm in Antibody Structure Prediction

Klaus Liedl, head of the Department of General, Inorganic and Theoretical Chemistry, collaborating with the FZ HPC, was granted a PRACE allocation of 68 million core hours for antibody binding property research on Piz Daint of the Swiss National Supercomputing Centre (CSCS).

Antibodies are a central part of the adaptive immune system, which is responsible for defending against pathogens such as viruses and bacteria in the human body. An essential process of the immune system is the affinity maturation of antibodies, which occurs after the first contact with the antigen. During affinity maturation, through several rounds of somatic hypermutation, the body produces antibodies with higher specificity and affinity. This leads to a very precise and efficient detection of pathogens, but also results in a lower effectiveness of this immune response in the case of mutations in viruses or other pathogens. This problem is becoming obvious due to the current development of the coronavirus pandemic. The immunity of both recovered and vaccinated people is impaired by the high specificity of the antibodies raised by the body against the virus through virus mutations.

By expanding the repertoire of cutting-edge simulation techniques, the research team of Klaus Liedl wants to achieve a complete description of the conformations, thermodynamics and kinetics of the entire binding region of antibodies in solution. These findings will have far-reaching implications for the field of antibody design and biotherapeutic development as they provide new understandings of the binding site, antibody-antigen recognition and their respective dynamics.

The researchers plan to use the dynamics of the binding region to improve structure prediction and understanding of the binding properties of antibodies and their specificity. The knowledge gained will also be used to optimize the characteristics that are important for the production and effectiveness of antibodies. In addition, a better understanding of these properties will help to better predict the detection of mutated pathogens and to perfectly match the specificity of therapeutic antibodies against pathogens and their mutations.

Prof. Klaus Liedl, chair of Theoretical Chemistry and head of the Department of General, Inorganic and Theoretical Chemistry at the University of Innsbruck was granted a PRACE Access project for simulating and investigating these binding properties. Collaborating with the FZ HPC, this project will employ a total of 68 million core hours on the Tier-0 supercomputer Piz Daint at the Swiss National Supercomputing Centre (CSCS).

For the success of the proposal it was essential that the research group is able to assemble their computer systems themselves and to adapt them to particularly challenging problems. This makes it possible to compete with elite universities with comparatively little money and allowed the research team to achieve preliminary results that successfully convinced the reviewers to grant large amounts of super computing time.

Key Information:

  • Project duration: October 1st 2021 – September 30th 2022
  • Computing time: ~68 million core hours on Piz Daint
  • PI: Klaus Liedl (Theoretical Chemistry)
  • Co-PIs: Monica Fernández Quintero (Theoretical Chemistry), Philipp Gschwandtner (FZ HPC), Yin Wang (Theoretical Chemistry)
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