© UDE

Project Area B - Chemical Biology

Prof. Dr. Elsa Sánchez-García

Fakultät Bio- und Chemieingenieurwesen

Technische Universität Dortmund


Email

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

julio.vieyto-nunez@tu-dortmund.de

Dr. Yasser Almeida-Hernandez

yasser.almeida@tu-dortmund.de

Dr. Joel Mieres Pérez

joel.mieresperez@tu-dortmund.de

Publications

    Journal articles

  • Beaufort, Nathalie; Ingendahl, Linda; Merdanovic, Melisa; Schmidt, Andree; Podlesainski, David; Richter, Tim; Neumann, Thorben; Kuszner, Michael; Vetter, Ingrid R.; Stege, Patricia; Burston, Steven G.; Filipovic, Anto; Ruiz-Blanco, Yasser B.; Bravo Rodriguez, Kenny; Mieres-Perez, Joel; Beuck, Christine; Uebel, Stephan; Zobawa, Monika; Schillinger, Jasmin; Malik, Rainer; Todorov-Völgyi, Katalin; Rey, Juliana; Roberti, Annabell; Hagemeier, Birte; Wefers, Benedikt; Müller, Stephan A.; Wurst, Wolfgang; Sanchez-Garcia, Elsa; Zimmermann, Alexander; Hu, Xiao-Yu; Clausen, Tim; Huber, Robert; Lichtenthaler, Stefan F.; Schmuck, Carsten; Giese, Michael; Kaiser, Markus; Ehrmann, Michael; Dichgans, Martin
    Rational correction of pathogenic conformational defects in HTRA1
    In: Nature Communications Vol. 15 (2024) Nr. 1, 5944
  • Day, Matthew; Tetik, Bilal; Parlak, Milena; Almeida-Hernández, Yasser; Räschle, Markus; Kaschani, Farnusch; Siegert, Heike; Marko, Anika; Sanchez-Garcia, Elsa; Kaiser, Markus; Barker, Isabel A.; Pearl, Laurence H.; Oliver, Antony W.; Boos, Dominik
    TopBP1 utilises a bipartite GINS binding mode to support genome replication
    In: Nature Communications Vol. 15 (2024) Nr. 1, 1797
  • Ruiz-Blanco, Yasser B.; Agüero-Chapin, Guillermin; Romero-Molina, Sandra; Antunes, Agostinho; Olari, Lia-Raluca; Spellerberg, Barbara; Münch, Jan; Sanchez-Garcia, Elsa
    ABP-Finder : A Tool to Identify Antibacterial Peptides and the Gram-Staining Type of Targeted Bacteria
    In: Antibiotics Vol. 11 (2022) Nr. 12, 1708
  • Rey, Juliana; Breiden, Maike; Lux, Vanda; Bluemke, Anika; Steindel, Maike; Ripkens, Kamilla; Möllers, Bastian; Bravo Rodriguez, Kenny; Boisguerin, Prisca; Volkmer, Rudolf; Mieres-Perez, Joel; Clausen, Tim; Sánchez-García, Elsa; Ehrmann, Michael
    An allosteric HTRA1-calpain 2 complex with restricted activation profile
    In: Proceedings of the National Academy of Sciences of the United States of America (PNAS) Vol. 119 (2022) Nr. 14, e2113520119
  • Harms, Mirja; Hansson, Rikke Fabech; Carmali, Sheiliza; Almeida-Hernández, Yasser; Sanchez-Garcia, Elsa; Münch, Jan; Zelikin, Alexander N.
    Dimerization of the Peptide CXCR4-Antagonist on Macromolecular and Supramolecular Protraction Arms Affords Increased Potency and Enhanced Plasma Stability
    In: Bioconjugate Chemistry Vol. 33 (2022) Nr. 4, pp. 594 - 607
  • Romero-Molina, Sandra; Ruiz-Blanco, Yasser B.; Mieres-Perez, Joel; Harms, Mirja; Münch, Jan; Ehrmann, Michael; Sanchez-Garcia, Elsa
    PPI-Affinity : A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity
    In: Journal of Proteome Research Vol. 21 (2022) Nr. 8, pp. 1829 - 1841
  • Böhm, Miriam; Killinger, Kerstin; Dudziak, Alexander; Pant, Pradeep; Jänen, Karolin; Hohoff, Simone; Mechtler, Karl; Örd, Mihkel; Loog, Mart; Sánchez-García, Elsa; Westermann, Stefan
    Cdc4 phospho-degrons allow differential regulation of ame1ceⁿp⁻u protein stability across the cell cycle
    In: eLife Vol. 10 (2021) e67390
  • Preprints

  • Brenner, Joel Cyrille; Zirden, Linda; Almeida-Hernandez, Yasser; Kaschani, Farnusch; Kaiser, Markus; Sanchez-Garcia, Elsa; Poepsel, Simon; Hellerschmied-Jelinek, Doris
    Conformational plasticity of a BiP-GRP94 chaperone complex
    (2024)