Scientists empower the computational design of biotherapeutics

9 May 2024
Scientists empower the computational design of biotherapeutics
Interaction of the staphylokinase-based drug candidate (left/green) with the plasmin protein (right/red) present in human blood. The amino acids of staphylokinase responsible for the interaction are shown by small spheres in different colors.

Scientists from the team of Josef Šivic at CIIRC CTU, in collaboration with researchers from Loschmidt Laboratories at Masaryk University and International Clinical Research Centre (ICRC Brno), and the team of Tomáš Pluskal at IOCB Prague, have developed a new method to improve the computational design of biotherapeutics.

The new method, called PPIformer, uses machine learning to more efficiently design proteins with better interaction properties, paving the way for significantly accelerating the development of new drugs for stroke and other diseases.

The results were presented at one of the world’s top machine learning conferences, ICLR 2024 in Vienna.

Read more in the CTU CIIRC press release.

The illustration of the proposed method that takes the protein interaction together with a target substitution as input (left) and predicts the effect of the substitution based on the predicted probabilities of possible amino acids (right).

  • Original article: A. Bushuiev, R. Bushuiev, P. Kouba, A. Filkin, M. Gabrielova, M. Gabriel, J. Sedlar, T. Pluskal, J. Damborsky, S. Mazurenko, J. Sivic, Learning to design protein-protein interactions with enhanced generalization, International Conference on Learning Representations (ICLR), 2024. 

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