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List of works by Matthias Ullmann

A mathematical view on the decoupled sites representation

scientific article published on 25 February 2012

A molecular mechanics force field for biologically important sterols

scientific article published in October 2005

ATP binding enables broad antibiotic selectivity of aminoglycoside phosphotransferase(3')-IIIa: an elastic network analysis

scientific article published on 06 April 2011

An ensemble of rapidly interconverting orientations in electrostatic protein-peptide complexes characterized by NMR spectroscopy.

scientific article published on 6 February 2014

An extended dead-end elimination algorithm to determine gap-free lists of low energy states.

scientific article published in November 2007

Anaerobic Microbial Degradation of Hydrocarbons: From Enzymatic Reactions to the Environment

scientific article

Assessing density functional theory in real-time and real-space as a tool for studying bacteriochlorophylls and the light-harvesting complex 2

scientific article published on 01 October 2019

Breaking Benzene Aromaticity-Computational Insights into the Mechanism of the Tungsten-Containing Benzoyl-CoA Reductase.

scientific article

Catalytic mechanism of the glycyl radical enzyme 4-hydroxyphenylacetate decarboxylase from continuum electrostatic and QC/MM calculations

scientific article published on 24 September 2013

CoMoDo: identifying dynamic protein domains based on covariances of motion

scientific article published on 12 May 2015

Comparing the rates and the activation parameters for the forward reaction between the triplet state of zinc cytochrome c and cupriplastocyanin and the back reaction between the zinc cytochrome c cation radical and cuproplastocyanin

scientific article published on 01 February 1999

Continuum electrostatic investigations of charge transfer processes in biological molecules using a microstate description

scientific article published in January 2011

Cysteine as a modulator residue in the active site of xenobiotic reductase A: a structural, thermodynamic and kinetic study

scientific article

DNA-induced dimerization of poly(ADP-ribose) polymerase-1 triggers its activation

scientific article published on 01 November 2005

Density functional calculation of p K(a) values and redox potentials in the bovine Rieske iron-sulfur protein

scientific article

Differential Effects of Cholesterol, Ergosterol and Lanosterol on a Dipalmitoyl Phosphatidylcholine Membrane: A Molecular Dynamics Simulation Study

article

Effects of pH on protein association: modification of the proton-linkage model and experimental verification of the modified model in the case of cytochrome c and plastocyanin

scientific article published in November 2001

Effects of single and double mutations in plastocyanin on the rate constant and activation parameters for the rearrangement gating the electron-transfer reaction between the triplet state of zinc cytochrome c and cupriplastocyanin

scientific article published in June 1998

Electron transfer between the quinones in the photosynthetic reaction center and its coupling to conformational changes.

scientific article published in August 2000

Electrostatic models for computing protonation and redox equilibria in proteins.

scientific article published in January 1999

Electrostatic potential at the retinal of three archaeal rhodopsins: implications for their different absorption spectra

scientific article

Energetics of electron-transfer and protonation reactions of the quinones in the photosynthetic reaction center of Rhodopseudomonas viridis.

scientific article

Experimental and DFT studies: novel structural modifications greatly enhance the solvent sensitivity of live cell imaging dyes

scientific article published on 5 October 2007

Glycerol dehydratation by the B12-independent enzyme may not involve the migration of a hydroxyl group: a computational study

scientific article published on 08 June 2012

Influence of the membrane potential on the protonation of bacteriorhodopsin: insights from electrostatic calculations into the regulation of proton pumping.

scientific article published in September 2006

Investigating the mechanisms of photosynthetic proteins using continuum electrostatics

scientific article (publication date: 14 May 2008)

Kinetic characterization of xenobiotic reductase A from Pseudomonas putida 86.

scientific article published in December 2009

Loss of electrostatic interactions causes increase of dynamics within the plastocyanin-cytochrome f complex

scientific article

Low potential enzymatic hydride transfer via highly cooperative and inversely functionalized flavin cofactors

scientific article published on 06 May 2019

MCMap-A Computational Tool for Mapping Energy Landscapes of Transient Protein-Protein Interactions

scientific article published on 18 June 2018

McVol - a program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm.

scientific article published on 22 July 2009

Mechanisms and Specificity of Phenazine Biosynthesis Protein PhzF.

scientific article

Molecular dynamics simulation of HIV-1 fusion domain-membrane complexes: Insight into the N-terminal gp41 fusion mechanism

scientific article published on 16 July 2012

Negatively charged residues and hydrogen bonds tune the ligand histidine pKa values of Rieske iron-sulfur proteins

scientific article published in October 2004

Partitioning of amino-acid analogues in a five-slab membrane model.

scientific article published on 28 June 2008

Photoswitching of the Fluorescent Protein asFP595: Mechanism, Proton Pathways, and Absorption Spectra

scientific article published on 01 January 2007

Poly(ADP-ribose) polymerase-1 dimerizes at a 5' recessed DNA end in vitro: a fluorescence study.

scientific article published on October 2003

Profile Hidden Markov Models for Analyzing Similarities and Dissimilarities in the Bacterial Reaction Center and Photosystem II†

scientific article published on 17 February 2009

Proton-transfer pathways in photosynthetic reaction centers analyzed by profile hidden markov models and network calculations

scientific article published on 13 March 2009

PyCPR - a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.

scientific article

Redox-linked protonation state changes in cytochrome bc1 identified by Poisson–Boltzmann electrostatics calculations

scientific article published on 31 January 2007

Role of hydrophobic interactions in the encounter complex formation of the plastocyanin and cytochrome f complex revealed by paramagnetic NMR spectroscopy.

scientific article

Simulating the proton transfer in gramicidin A by a sequential dynamical Monte Carlo method.

scientific article published on 30 September 2008

Simultaneous true, gated, and coupled electron-transfer reactions and energetics of protein rearrangement

scientific article published on 17 September 2011

Spectroscopic, kinetic, and mechanistic study of a new mode of coordination of indole derivatives to platinum(II) and palladium(II) ions in complexes.

scientific article

Structure and Function of 4-Hydroxyphenylacetate Decarboxylase and Its Cognate Activating Enzyme.

scientific article published on 10 March 2016

Structure and Function of the Unusual Tungsten Enzymes Acetylene Hydratase and Class II Benzoyl-Coenzyme A Reductase

scientific article published on 10 March 2016

Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase

scientific article

The Charge Distribution on a Protein Surface Determines Whether Productive or Futile Encounter Complexes Are Formed

scientific article published on 01 March 2021

The Electronically Excited States of LH2 Complexes from Rhodopseudomonas acidophila Strain 10050 Studied by Time-Resolved Spectroscopy and Dynamic Monte Carlo Simulations. I. Isolated, Non-Interacting LH2 Complexes

scientific article published on 22 June 2011

The Electronically Excited States of LH2 Complexes from Rhodopseudomonas acidophila Strain 10050 Studied by Time-Resolved Spectroscopy and Dynamic Monte Carlo Simulations. II. Homo-Arrays Of LH2 Complexes Reconstituted Into Phospholipid Model Membran

scientific article published on 22 June 2011

The alpha helix dipole: screened out?

scientific article published in June 2005

The dynamic complex of cytochrome c6 and cytochrome f studied with paramagnetic NMR spectroscopy

scientific article published on 28 March 2014

The influence of a transmembrane pH gradient on protonation probabilities of bacteriorhodopsin: the structural basis of the back-pressure effect

scientific article published in June 2004

Theoretical investigation of the behavior of titratable groups in proteins

scientific article published on 12 April 2006

Understanding the energetics of helical peptide orientation in membranes.

scientific article

Visualization of the encounter ensemble of the transient electron transfer complex of cytochrome c and cytochrome c peroxidase

scientific article published on 01 January 2010

pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states

scientific article

pH-dependent molecular dynamics of vesicular stomatitis virus glycoprotein G.

scientific article published on 10 August 2012

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