Institutions of the University of Bayreuth
Professor Bioinformatics/Structural Biology

Bombarda, Elisa ; Ullmann, G. Matthias:
Continuum electrostatic investigations of charge transfer processes in biological molecules using a microstate description.
In: Faraday Discussions. Vol. 148 (2011) . - pp. 173-193.
DOI: https://doi.org/10.1039/c003905e

Culka, Martin:
Computational Modeling of Enzyme Reactions Involved in Aromatic Compound Metabolism.
Bayreuth , 2017 . - V, 52 p.
( Doctoral thesis, 2017 , Universität Bayreuth, Fakultät für Biologie, Chemie und Geowissenschaften)

Culka, Martin ; Gisdon, Florian J. ; Ullmann, G. Matthias:
Computational Biochemistry : Enzyme Mechanisms Explored.
In: Karabencheva-Christova, Tatyana (ed.): Structural and Mechanistic Enzymology. - Cambridge : Elsevier Academic Press, 2017 . - pp. 77-112 . - (Advances in Protein Chemistry and Structural Biology ; 109 )
DOI: https://doi.org/10.1016/bs.apcsb.2017.04.004

Di Savino, Antonella ; Förster, Johannes ; Ullmann, G. Matthias ; Ubbink, Marcellus:
Enhancing the population of the encounter complex affects protein complex formation efficiency.
In: The FEBS Journal. Vol. 289 (2022) Issue 2 . - pp. 535-548.
DOI: https://doi.org/10.1111/febs.16159

Di Savino, Antonella ; Förster, Johannes ; Ullmann, G. Matthias ; Ubbink, Marcellus:
The Charge Distribution on a Protein Surface Determines Whether Productive or Futile Encounter Complexes Are Formed.
In: Biochemistry. Vol. 60 (2021) Issue 10 . - pp. 747-755.
DOI: https://doi.org/10.1021/acs.biochem.1c00021

di Savino, Antonella ; Förster, Johannes ; la Haye, Thijmen ; Blok, Anneloes ; Timmer, Monika ; Ullmann, G. Matthias ; Ubbink, Marcellus:
Efficient Encounter Complex Formation and Electron Transfer to Cytochrome c Peroxidase with an Additional, Distant Electrostatic Binding Site.
In: Angewandte Chemie. Vol. 132 (2020) Issue 51 . - pp. 23439-23443.
DOI: https://doi.org/10.1002/ange.202010006

Förster, Johannes M.:
Influence of Electrostatics on Protein-Protein Interactions of Photosynthetic Proteins.
Bayreuth , 2018 . - X, 151 p.
( Doctoral thesis, 2018 , Universität Bayreuth, Bayreuther Graduiertenschule für Mathematik und Naturwissenschaften - BayNAT)
DOI: https://doi.org/10.15495/EPub_UBT_00003575

Feliks, Mikolaj:
Computational Modeling of Catalytic Mechanisms of Glycyl Radical Enzymes.
Bayreuth , 2014 . - 86 p.
( Doctoral thesis, 2014 , Universität Bayreuth, Fakultät für Biologie, Chemie und Geowissenschaften)

Gisdon, Florian J.:
Comparative Computational Study of Serine Peptidase and Cysteine Peptidase Mechanisms.
Bayreuth , 2022 . - vi, 180, I p.
( Doctoral thesis, 2022 , Universität Bayreuth, Fakultät für Biologie, Chemie und Geowissenschaften)
DOI: https://doi.org/10.15495/EPub_UBT_00006419

Gisdon, Florian J. ; Bombarda, Elisa ; Ullmann, G. Matthias:
Serine and Cysteine Peptidases: So Similar, Yet Different : How the Active-Site Electrostatics Facilitates Different Reaction Mechanisms.
In: The Journal of Physical Chemistry B. Vol. 126 (2022) Issue 22 . - pp. 4035-4048.
DOI: https://doi.org/10.1021/acs.jpcb.2c01484

Gisdon, Florian J. ; Feiler, Christian G. ; Kempf, Oxana ; Förster, Johannes ; Haiss, Jonathan ; Blankenfeldt, Wulf ; Ullmann, G. Matthias ; Bombarda, Elisa:
Structural and Biophysical Analysis of the Phytochelatin-Synthase-Like Enzyme from Nostoc sp. Shows That Its Protease Activity is Sensitive to the Redox State of the Substrate.
In: ACS Chemical Biology. Vol. 17 (2022) Issue 4 . - pp. 883-897.
DOI: https://doi.org/10.1021/acschembio.1c00941

Gisdon, Florian J. ; Culka, Martin ; Ullmann, G. Matthias:
PyCPR – a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.
In: Journal of Molecular Modeling. Vol. 22 (2016) . - 242.
DOI: https://doi.org/10.1007/s00894-016-3116-8

Kempf, Oxana ; Ullmann, G. Matthias ; Schobert, Rainer ; Kempf, Karl ; Bombarda, Elisa:
Chemoselective Attachment of the Water-Soluble Dark Quencher Hydrodabcyl to Amino Groups in Peptides and Preservation of Its Spectroscopic Properties over a Wide pH Range.
In: ACS Omega. Vol. 6 (2021) Issue 48 . - pp. 32896-32903.
DOI: https://doi.org/10.1021/acsomega.1c04891

Roy, Rajeev Ranjan ; Ullmann, G. Matthias:
Virtual Model Compound Approach for Calculating Redox Potentials of [Fe₂S₂]-Cys₄ Centers in Proteins – Structure Quality Matters.
In: Journal of Chemical Theory and Computation. Vol. 19 (2023) Issue 23 . - pp. 8930-8941.
DOI: https://doi.org/10.1021/acs.jctc.3c00779

Schweiger, Andreas ; Ullmann, G. Matthias ; Nürk, Nicolai ; Triebel, Dagmar ; Schobert, Rainer ; Rambold, Gerhard:
Chemical properties of key metabolites determine the global distribution of lichens.
In: Ecology Letters. Vol. 25 (2022) Issue 2 . - pp. 416-426.
DOI: https://doi.org/10.1111/ele.13930

Schock, Marina ; Schmidt, Steffen ; Ersfeld, Klaus:
Novel Cytoskeleton-Associated Proteins in Trypanosoma brucei Are Essential for Cell Morphogenesis and Cytokinesis.
In: Microorganisms. Vol. 9 (2021) Issue 11 . - 2234.
DOI: https://doi.org/10.3390/microorganisms9112234

Schelter, Ingo ; Förster, Johannes ; Gardiner, Alastair T. ; Roszak, Aleksander W. ; Cogdell, Richard J. ; Ullmann, G. Matthias ; de Queiroz, Thiago Branquinho ; Kümmel, Stephan:
Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2.
In: The Journal of Chemical Physics. Vol. 151 (2019) Issue 13 . - 134114.
DOI: https://doi.org/10.1063/1.5116779