CRC 1093 - Publications Project A7

Area A: Chemical Ligands and Method

Publications by Prof. Dr. Daniel Hoffmann

Project A7:
Pareto-optimization of protein-surface targeting supramolecular binders with hetero-avidity

N. Tötsch, D. Hoffmann: Classifier uncertainty: evidence, potential impact, and probabilistic treatment. PeerJ Computer Science 2021. 7:e398

N. Toetsch, D. Hoffmann: Bayesian Data Integration Questions Classic Study on Protease Self-Digest Kinetics. ACS Omega. 2020 Jun22,

J. N. Grad, A. Gigante, C. Wilms, J. N. Dybowski, L. Ohl, C. Ottmann , C. Schmuck, D. Hoffmann: Locating Large, Flexible Ligands on Proteins. J Chem Inf Model. 2018 Jan 11. doi: 10.1021/acs.jcim.7b00413.

M. Nemec, D. Hoffmann: Quantitative assessment of molecular dynamics sampling for flexible systems. J Chem Theory Comput. 2017 Jan 13. doi: 10.1021/acs.jctc.6b00823.

M. Klammer, J.N. Dybowski, D. Hoffmann, C. Schaab: Identification of significant features by the global mean rank test. PLoS One. 2014 9(8):e104504.

R. Rebollido-Rios, S. Bandari, C. Wilms, S. Jakuschev, A. Vortkamp, K. Grobe, D. Hoffmann: Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase. PLoS Comput Biol. 2014 07;10(7):e1003707.

D. Heider, J. N. Dybowski, C. Wilms, D. Hoffmann: A simple structure-based model for the prediction of HIV-1 co-receptor tropism. BioData Min. 2014 Aug 1;7:14. doi: 10.1186/1756-0381-7-14. eCollection 2014.

A. Matena, C. Sinnen, J. van den Boom, C. Wilms, J.N. Dybowski, R. Maltaner, J.W. Mueller, N.M. Link, D. Hoffmann, P. Bayer: Transient domain interactions enhance the affinity of the mitotic regulator Pin1 toward phosphorylated peptide ligands. Structure. 2013, Oct 8;21(10):1769-77.

Q.-Q. Jiang, L. Bartsch, W. Sicking, P. R. Wich, D. Heider, D. Hoffmann, C. Schmuck: A new approach to inhibit human β-Tryptase by protein surface binding of four-armed peptide ligands with two different sets of arms. Org. Biomol. Chem. 2013, 11, 1631-1639.

D. Grum, S. Franke, O. Kraff, D. Heider, A. Schramm, D. Hoffmann, P. Bayer: Design of a modular protein-based MRI contrast agent for targeted application. PLoS One. 2013, Jun 6;8(6):e65346.

S. Genheden, O. Kuhn, P. Mikulskis, D. Hoffmann, U. Ryde: The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant. J. Chem. Inform. Mod. 2012, 52, 2079-2088.

G. Lattig-Tunnemann, M. Prinz, D. Hoffmann, J. Behlke, C. Palm-Apergi, I. Morano, H. D. Herce, M. C. Cardoso: Backbone rigidity and static presentation of guanidinium groups increases cellular uptake of arginine-rich cell-penetrating peptides. Nat. Commun. 2011, 2, 453.

 J. N. Dybowski, D. Heider, D. Hoffmann: Prediction of co-receptor usage of HIV-1 from genotype. PLoS Comput. Biol. 2010, 6:e1000743.

W. Gronwald, T. Hohm, D. Hoffmann: Evolutionary Pareto-optimization of stably folding peptides. BMC Bioinformatics 2008, 9,109.

J. Jacob, K. Gessler, D. Hoffmann, H. Sanbe, K. Koizumi, S. M. Smith, T. Takaha, W. Saenger: Strain-induced flips of glucoses in cyclodecaamylose and higher homologues. Angew. Chem. Int. Ed. 1998, 37, 605-609.

D. Hoffmann, B. Kramer, T. Washio, T. Steinmetzer, M. Rarey, T. Lengauer: Two-Stage Method for Protein-Ligand Docking. J. Med. Chem. 1999, 42, 4422-4433.

More Publications Area A

  • Project A1
    Protein-recognition by supramolecular ligands from focused combinatorial libraries (Carsten Schmuck)
  • Project A2
    Natural products as starting structures for the development of supramolecular ligands (Markus Kaiser)
  • Project A3
    Designed copolymers and molecular tweezers for protein surface recognition (Thomas Schrader)
  • Project A5
    Protein-specific nanoparticles for cellular uptake (Matthias Epple)
  • Project A6
    DNA-based nanocontainers for predesigned spatial confinement of proteins (Barbara Saccà)
  • Project A7
  • Project A8
    Exploring protein-recognition by supramolecular binders with MD and QM/MM methods (Elsa Sánchez-Garcia)
  • Project A9
    Raman spectroscopic monitoring of protein recognition by supramolecular ligands (Sebastian Schlücker)

Biological Targets Publications Area B

  • Project B1
    Supramolecular ligands modulate assembly and function of HtrA proteases (Michael Ehrmann)
  • Project B2
    Probing mechanisms of the Cdc48/p97 segregase with designed supramolecular ligands (Hemmo Meyer)
  • Project B3
    Supramolecular specific inhibitors of intestinal proteases against ischemia/reperfusion injury (Herbert de Groot)
  • Project B4
    Modulation of 14-3-3 protein-protein interactions by supramolecular chemistry (Christian Ottmann)
  • Project B5
    Dissection and modulation of (patho)biological Survivin functions by supramolecular ligands (Shirley Knauer)
  • Project B6
    Targeting centromer recruitment of mitotic regulators by supramolecular ligands (Andrea Musacchio)