CRC 1093 - Principal Investigator Daniel Hoffmann

Prof. Dr. Daniel Hoffmann

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Phone: +49 201 183 4391


Centre for Medical Biotechnology (ZMB)
Faculty of Biology
University of Duisburg-Essen

Area A: Chemical Ligands and Methods A7: Pareto-optimization of protein-surface targeting supramolecular binders with hetero-avidity

The challenge to achieve optimized hetero-avidity of larger protein surface binders will be adressed in A7 with a focus on combinatorial approaches. Protein binders are analyzed as librar-ies of different molecular recognition units covalently attached to a flexible generic scaffold. Various limiting criteria such as positive cooperativity and protein specificity are treated independently, and combined in a Pareto-optimization procedure. Special attention will be paid to the treatment of sol-vent and entropy effects. Relationships between binder composition and experimental assays will be statistically analyzed, including training of machine learning models.

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Curriculum Vitae

Professional career

Scientific education and degrees


Selected Publications

M. Saeedghalati, F. Farahpour, B. Budeus, A. Lange, A. M. Westendorf, M. Seifert, R. Küppers, D. Hoffmann: Quantitative Comparison of Abundance Structures of Generalized Communities: From B-Cell Receptor Repertoires to Microbiomes. PLoS Comput. Biol. 2017, Jan; 13:e1005362.

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

H. Kefalakes, B. Budeus, A. Walker, C. Jochum, G. Hilgard, A. Heinold, F. M. Heinemann, G. Gerken, D. Hoffmann, J. Timm: Adaptation of the hepatitis B virus core protein to CD8(+) T-cell selection pressure. Hepatology. 2015 Jul;62(1):47–56.

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

J N Dybowski, D Heider, and D Hoffmann. Prediction of co-receptor usage of HIV-1 from genotype. PLoS Comput. Biol. 2010, 6(4):e1000743, Apr 2010.

T. Hohm, P. Limbourg, and D. Hoffmann. A multiobjective evolutionary method for the design of peptidic mimotopes. J. Comput. Biol. 2006, 13:113–125.

S. Wefing, V. Schnaible, D. Hoffmann: SearchXLinks – A Program for Identifying Crosslinks or Disulfide Bonds in Proteins from Mass Spectra. Analytical Chemistry. 2006, 78: 1235–1241.

V. Schnaible, S. Wefing, A. Resemann, D. Suckau, A. Bücker, S. Wolf-Kümmeth, and Hoffmann D. Screening for Disulfide Bonds in Proteins by MALDI-ISD and LIFT-TOF/TOF-MS. Analytical Chemistry. 2002, 74:4980–4988.

D. Hoffmann, B. Kramer, T. Washio, T. Steinmetzer, M. Rarey, and T. Lengauer. Two-stage method for protein-ligand docking. J. Med. Chem. 1999, 42:4422–4433.

D. Hoffmann, H. Flörke: A structural role for glycosylation: lessons from the hp-model. Folding & Design. 1998; 3: 337–343.