B04
Project Area B - Chemical Biology
Prof. Dr. Elsa Sánchez-García
Fakultät Bio- und Chemieingenieurwesen
Technische Universität Dortmund
Hybrid computational strategies for the study of cell states
Computational approaches play an essential role in the study of biological processes and well as in the design and optimization of compounds that can be used for monitoring and regulating such processes. In project B04, we employ novel in-house as well as state-of-the-art computational methodologies including machine learning tools, docking techniques, molecular dynamics simulations and free energy calculations to deliver molecular insights into protein-protein interactions relevant for cell transitions. In addition, our computational strategy allows the in-silico design of chemical tools and inhibitors targeting these processes. This way, in close collaboration with our chemistry and biology experimental partners, we contribute a deeper mechanistic understanding of key cellular processes.
Project Members
Julio Cesar Vieyto Nuñez
Dr. Yasser Almeida-Hernandez
Dr. Joel Mieres Pérez
Publications
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Rational correction of pathogenic conformational defects in HTRA1In: Nature Communications Vol. 15 (2024) Nr. 1, 5944Online Full Text: dx.doi.org/ (Open Access)
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TopBP1 utilises a bipartite GINS binding mode to support genome replicationIn: Nature Communications Vol. 15 (2024) Nr. 1, 1797Online Full Text: dx.doi.org/; Online Full Text: dx.doi.org/ (Open Access)
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ABP-Finder : A Tool to Identify Antibacterial Peptides and the Gram-Staining Type of Targeted BacteriaIn: Antibiotics Vol. 11 (2022) Nr. 12, 1708Online Full Text: dx.doi.org/ (Open Access)
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An allosteric HTRA1-calpain 2 complex with restricted activation profileIn: Proceedings of the National Academy of Sciences of the United States of America (PNAS) Vol. 119 (2022) Nr. 14, e2113520119Online Full Text: dx.doi.org/ Online Full Text (Open Access)
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Dimerization of the Peptide CXCR4-Antagonist on Macromolecular and Supramolecular Protraction Arms Affords Increased Potency and Enhanced Plasma StabilityIn: Bioconjugate Chemistry Vol. 33 (2022) Nr. 4, pp. 594 - 607Online Full Text: dx.doi.org/
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PPI-Affinity : A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding AffinityIn: Journal of Proteome Research Vol. 21 (2022) Nr. 8, pp. 1829 - 1841Online Full Text: dx.doi.org/ (Open Access)
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Cdc4 phospho-degrons allow differential regulation of ame1ceⁿp⁻u protein stability across the cell cycleIn: eLife Vol. 10 (2021) e67390Online Full Text: dx.doi.org/ (Open Access)
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Conformational plasticity of a BiP-GRP94 chaperone complex(2024)Online Full Text: dx.doi.org/ Online Full Text (Open Access)