Publications & Conferences

Ayyildiz, M., Noske, J., Gisdon, F.J., Kynast, J.P., Höcker, B. (2024) Complementary evaluation of computational methods for predicting single residue effects on peptide binding specificities. bioRxiv, doi: 10.1101/2024.10.18.619108

Stark, Y., Menard, F., Jeliazkov, J.R., Ernst, P., Chembath, A., Ashraf, M., Hine, A.V., Plückthun, A. (2024) Modular binder technology by NGS-aided, high-resolution selection in yeast of designed armadillo modules. Proc. Natl. Acad. Sci. USA, doi: 10.1073/pnas.2318198121

Cucuzza, S., Sitnik, M., Jurt, S., Michel, E., Dai, W., Müntener, T., Ernst, P., Häussinger, D., Plückthun, A., Zerbe, O. (2023) Unexpected dynamics in femtomolar complexes of binding proteins with peptides. Nat. Commun., doi: 10.1038/s41467-023-43596-2

Kynast, J.P., Höcker, B. (2023) Atligator Web: A Graphical User Interface for Analysis and Design of Protein–Peptide Interactions. BioDesign Res., doi: 10.34133/bdr.0011

Michel, E., Cucuzza, S., Mittl, P.R.E., Zerbe, O., and Plückthun, A. (2023) Improved Repeat Protein Stability by Combined Consensus and Computational Protein Design. Biochemistry, doi: 10.1021/acs.biochem.2c00083

Noske, J., Kynast, J.P., Lemm, D., Schmidt, S., Höcker, B. (2022) PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design. Prot. Sci., doi: 10.1002/pro.4516

Kynast, J.P., Schwägerl, F., Höcker, B. (2022) ATLIGATOR: Editing protein interactions with an atlas-based approach. Bioinformatics, doi: 10.1093/bioinformatics/btac685

Ferruz, N., Schmidt, S., Höcker, B. (2022) ProtGPT2 is a deep unsupervised language model for protein design. Nat. Commun., doi: 10.1038/s41467-022-32007-7

Chembath, A., Wagstaffe, B. P. G., Ashraf, M., Amaral, M. M. F., Frigotto, L. & Hine, A. V. (2022) Nondegenerate Saturation Mutagenesis: Library Construction and Analysis via MAX and ProxiMAX Randomization. Directed Evolution: Methods in Molecular Biology, doi: 10.1007/978-1-0716-2152-3_3

Gisdon, J.F., Kynast, J.P., Ayyildiz, M., Hine, A.V., Plückthun, A., Höcker B. (2022) Modular peptide binders - development of a predective technology as alternative for reagent antibodies. Biol. Chem., doi: 10.1515/hsz-2021-0384

Ferruz, N., Noske, J., Höcker, B. (2021) Protlego: A Python package for the analysis and design of chimeric proteins. Bioinformatics, doi: 10.1093/bioinformatics/btab253

Hansen, S., Ernst, P., König, S. L. B., Reichen, C., Ewald, C., Nettels, D., Mittl, P. R. E., Schuler, B. and Plückthun, A. (2018) Curvature of designed armadillo repeat proteins allows modular peptide binding. J. Struct. Biol., doi: 10.1016/j.jsb.2017.08.009

Hansen, S., Kiefer, J. D., Madhurantakam, C., Mittl, P. R. E. and Plückthun, A. (2017) Structures of designed armadillo repeat proteins binding to peptides fused to globular domains. Protein Sci., doi: 10.1002/pro.3229

Ferreira-Amaral, M.M., Frigotto, L. and Hine, A.V. (2017) Beyond the natural proteome: nondegenerate saturation mutagenesis – methodologies and advantages. Meth. Enyzmol., doi: 10.1016/bs.mie.2016.10.005

Ernst, P. and Plückthun, A. (2017) Advances in the design and engineering of peptide-binding repeat proteins. Biol. Chem., doi: 10.1515/hsz-2016-0233

Frigotto, L., Smith, M.E., Brankin, C., Sedani, A., Cooper, S.E., Kanwar, N., Evans, D., Svobodova, S., Baar, C., Glanville, J, Ullman, C.G. and Hine, A.V. (2015) Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through Next Generation Sequencing. Antibodies, doi: 10.3390/antib4020088

Janzen, M., Noske, J. & Höcker, B. Predicting single residue effects on peptide binding specificities in designed Armadillo repeat proteins. 76th Mosbacher Kolloquium on AI-driven (r)evolution in structural biology & protein design, March 19th–22nd 2025, Mosbach / Baden, Germany

Wepfer, J., Loarer, G., Caflisch, A. & Plückthun, A. Computational design of sequence-specific peptide binders using AF2. 76th Mosbacher Kolloquium on AI-driven (r)evolution in structural biology & protein design, March 19th–22nd 2025, Mosbach / Baden, Germany

Hine, Anna V. New Formats for Reagent Antibodies. NextGen Biomed, 12–14th March 2025, London, UK

Plückthun, A. The design of evolution and the evolution of design. Biozentrum, University of Basel, 21st February 2025, Basel, Switzerland

Plückthun, A. Precision gene delivery through protein engineering. 28th ESACT Meeting, 23rd–26th June 2024, Edinburgh, Scotland

Höcker, B. Learning from nature how to design new proteins. Novo Nordisk Science Cluster Symposium: Data Science for Planetary and Human Health - The True Life Cycle of Multi-omics Data, 10th–12th June 2024, Copenhagen, Denmark

Kynast, J. Atlas-based analysis and design of amino-acid binding pockets. Rabensteiner Kolleg, 30th May-1st June 2024, Pottenstein, Germany

Plückthun, A. Binding proteins: the design of evolution and the evolution of design. Joint Symposium of the Taiwan Biophysical Society and INPEC, 22nd–23rd May 2024, Taipei, Taiwan

Plückthun, A. The design of evolution and the evolution of design. Symposium and Workshop on Directed Evolution of Proteins, 28th April–1st May 2024, Kosice, Slovakia

Plückthun, A. DARPin based therapies and gene-therapy-based antibody delivery. Paul-Martini-Stiftung (PMS) Workshop, 17th April 2024, Berlin, Germany

Plückthun, A. Binding proteins: the design of evolution and the evolution of design. Symposium of the Deutsches Krebsforschungszentrum (DKFZ), 15th April 2024, Heidelberg, Germany

Plückthun, A. Modular binding proteins. 10th Alpbach Workshop on Affinity Proteomics, 10th–14th March 2024, Alpbach, Austria

Plückthun, A. The synthetic biology of therapeutic proteins. Synthetic Biology UK 2023, 6th–7th November 2023, Bristol, UK

Plückthun, A. Therapeutic Proteins: From Engineering to in situ delivery. BioToP Conference, 19th–20th June 2023, Vienna, Austria

Plückthun, A. The design of evolution and the evolution of design. AFFINITY 2023, 5th–7th June 2023, Lisbon, Portugal

Plückthun, A. The evolution of design and the design of evolution. University of Minnesota, 8th March 2023, Minneapolis, USA

Noske, J. PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design. Poster presentation at Keystone Conference on Computational Modelling, March 2023, Banff, Canada

Kynast, J. P. Learn from Nature: Binding Site Design for Modular Peptide Binding. Poster presentation at Keystone Conference on Computational Modelling, March 2023, Banff, Canada

Ayyildiz, M. Computational design of specific binding pockets for phosphorylated amino acids within Armadillo repeat proteins. Poster presentation at 74th Mosbacher Kolloquium on Immune Engineering, March 2023, Mosbach / Baden, Germany

Plückthun, A. Binding proteins: Design of Evolution and Evolution of Design. Linderstroem-Lang Symposium: Frontiers in Protein Science, 18th November 2022

Chembath, A., Ashraf, M., Wagstaffe, B.P.G., Stark, Y., Michel, E., Rohrbach, A., Kynast, J. P., Gisdon, F., Ayyildiz, M., Höcker, B., Plückthun, A., Hine, A.V. Creating synthetic replacements for reagent antibodies. Synthetic Biology UK 2022, 7th–9th November 2022, Newcastle, UK

Plückthun, A. Design of therapeutic proteins. 23rd–27th October 2022, Upper Galilee, Israel

Plückthun, A. Binding proteins: Evolution of design and design of evolution. Workshop on Coiled-Coil, Fibrous & Repeat Proteins, Alpbach CuPiD Meeting, 4th–9th September 2022, Alpbach, Austria

Plückthun, A. Antibody Engineering & Therapeutics EUROPE. 7th–9th June 2022, Amsterdam, Netherlands

Parmeggiani, F., Pellarin, R., Larsen, A.P., Varadamsetty, G., Stumpp, M.T. & Plueckthun, A. Designed armadillo repeat proteins. Published as: US2011224100A1, US9365629B2, EP2198022A1