Theses

PhD Theses

27.	Behrendt, A. Physics- and data science-based computational predictive modeling to investigate molecular mechanisms in cholestatic liver diseases. Heinrich-Heine-University, Düsseldorf, 2024.
26.	Becker, D. Molecular determinants underlying substrate promiscuity and polymorphism in drug-metabolizing CYP enzymes. Heinrich-Heine-University, Düsseldorf, 2024.
25.	Dittrich, J. Molecular simulations on leaf anchor peptides and microgel carriers suitable for advanced/sustainable nutrient and herbicide delivery. Heinrich-Heine-University, Düsseldorf, 2023.
24.	Ahmad, S. Substrate access mechanism in a novel phospholipase A of Pseudomonas aeruginosa. Heinrich-Heine-University, Düsseldorf, 2022.
23.	Bonus, M. Computational modeling of function-determining protein-ligand interactions in adhesion receptors and ligand-gated ion channels.. Heinrich-Heine-University, Düsseldorf, 2022.
22.	Bickel, D. Computational drug design in natural leads to overcome drug resistance in targeted and pan-cancer therapy. Heinrich-Heine-University, Düsseldorf, 2021.
21.	Mulnaes, D. TopSuite: A meta-suite for protein structure prediction using deep neural networks.. Heinrich-Heine-University, Düsseldorf, 2020.
20.	Schott-Verdugo, S. Modeling of membrane proteins in a bilayer context: from system construction to structural prediction and dynamics. Heinrich-Heine-University, Düsseldorf, 2020.
19.	Frieg, B. Integrative modeling of function-associated molecular recognition in protein-ligand, protein-peptide, and protein-protein complexes. Heinrich-Heine-University, Düsseldorf, 2019.
18.	Verma, N. Energetics and dynamics of lipase A activation by the steric chaperone Lif in Pseudomonas aeruginosa. Heinrich-Heine-University, Düsseldorf, 2019.
17.	Kröger, T. Assay development and optimization for the validation and quantification of NHR2 tetramerization inhibitors and prediction of the binding mode. Heinrich-Heine-University, Düsseldorf, 2018.
16.	Pagani, G. Linking structure and dynamics of integrin αIIbβ3 to its biological function via molecular dynamics simulations and free energy calculations. Heinrich-Heine-University, Düsseldorf, 2018.
15.	Saini, J. Structural and dynamic insights into oxazolidinone binding, selectivity and resistance to the large ribosomal subunit. Heinrich-Heine-University, Düsseldorf, 2018.
14.	Ciupka, B.D. Functional state modulation in PPDK connected to long-range structural coupling and multimerization. Heinrich-Heine-University, Düsseldorf, 2017.
13.	Gertzen, C. Integrative modeling to determine the activity, molecular recognition, and membrane trafficking of the G-protein coupled bile acid receptor TG. Heinrich-Heine-University, Düsseldorf, 2016.
12.	Hanke, C. Conformational dynamics of the ligand-free state of a riboswitch investigated by molecular simulations. Heinrich-Heine-University, Düsseldorf, 2016.
11.	Ben-Shalom, I.Y. Approximate and efficient prediction of entropy changes upon complex formation. Heinrich-Heine-University, Düsseldorf, 2016.
10.	Ciglia, E. Inhibiting protein-protein interactions in Hsp90 dimerization as a novel approach for targeting cancer. Heinrich-Heine-University, Düsseldorf, 2015.
9.	Pfleger, C. Ensemble-based framework for analyzing dynamically dominated allostery. Heinrich-Heine-University, Düsseldorf, 2014.
8.	Rathi, P.C. Development of computational approaches for knowledge-driven protein engineering aimed at improving thermostability. Heinrich-Heine-University, Düsseldorf, 2014.
7.	Metz, A. Predicting and exploiting the determinants of protein/protein interactions to identify low-molecular weight inhibitors of RUNX1-ETO tetramerization. Heinrich-Heine-University, Düsseldorf, 2014.
6.	Kazemi, S. Entwicklung eines Docking-Verfahrens zur Berücksichtigung der Liganden- und Protein-Flexibilität durch einen elastischen Potentialgitter-Ansatz. Goethe-University, Frankfurt, 2014.
5.	Krüger, D. Computational knowledge-based prediction of protein-protein recognition. Heinrich-Heine-University, Düsseldorf, 2014.
4.	Radestock, S. Entwicklung eines rechnerischen Verfahrens zur Simulation der thermischen Entfaltung von Proteinen und zur Untersuchung ihrer Thermostabilitaet. Goethe University, Frankfurt am Main, 2010.
3.	Fulle, S. Constraint counting on RNA and ribosomal structures: Linking flexibility and function. Goethe University, Frankfurt am Main, 2010.
2.	Gonzalez-Ruiz, D. QCSPScore: a new scoring function for driving protein-ligand docking with quantitative chemical shift perturbations. Goethe University, Frankfurt am Main, 2009.
1.	Ahmed, A. Development of a normal mode-based geometric simulation approach for investigating the intrinsic mobility of proteins. Goethe University, Frankfurt am Main, 2009.

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Diploma / Master / Bachelor Theses

 

34.	Abdyli, E. Assessing protein structure prediction: Comparative analysis of leading protein modeling platforms with focus on loops Heinrich-Heine-Universität, Düsseldorf, 2024.
33.	Klostermann, K. Ligand influences on nicotinic acetylcholine receptor switching Heinrich-Heine-Universität, Düsseldorf, 2023.
32.	Willner, H. Targeted degradation of detrimental cellular content – Hijacking the autophagy pathway Heinrich-Heine-Universität, Düsseldorf, 2022.
31.	Helmy, K. Electrostatic influence of mutations of the mHCN2 channel on the gating behavior Heinrich-Heine-Universität, Düsseldorf, 2022.
30.	Wijaya, R. Interactions of the death receptor CD95 Heinrich-Heine-Universität, Düsseldorf, 2022.
30.	Koenig, F. Predicting residue-specific protein-protein interactions using machine learning Heinrich-Heine-Universität, Düsseldorf, 2021.
29.	Akter, S. Molecular simulations of membrane permeability of protein-protein interaction inhibitors Heinrich-Heine-Universität, Düsseldorf, 2020.
28.	Brack, J.-K. Untersuchung des agonistischen Effekts nativer Liganden auf TGR5 mittels Rigiditätsanalyse Martin-Luther-Universität, Halle-Wittenberg, 2018.
27.	Dittrich, J. Converging a knowledge-based scoring function: DrugScore2017 Hochschule Niederrhein, Krefeld, 2018.
26.	Eichler, I. Lipid translocation by multidrug resistance protein 3 Martin-Luther-Universität, Halle-Wittenberg, 2017.
25.	Ouald Chaib, A. Directed evolution and sequence-function relationships of P450 catalyzed non-natural carbene and nitrene transfer reactions Heinrich-Heine-Universität, Düsseldorf, 2017. (Exp. work performed at Caltech, CA, USA)
24.	Waeschenbach, L. Configurational free energy calculations of GPCR dimerization Heinrich-Heine-Universität, Düsseldorf, 2017.
23.	Loschwitz, J. Molekulardynamik-Simulationen freier Ligandendiffusion zur Bindemodenvorhersage von Protein-Protein-Interaktions-Modulatoren Heinrich-Heine-Universität, Düsseldorf, 2017.
22.	Nutschel, C. Large-scale analysis of protein thermostability: Bacillus subtilis lipase A as a test case Heinrich-Heine-Universität, Düsseldorf, 2016.
21.	Wolf, S. Development of a meta-tool for protein domain prediction Heinrich-Heine-Universität, Düsseldorf, 2016.
20.	Ludwig, R. Binding site comparison using deep neural networks Heinrich-Heine-Universität, Düsseldorf, 2016.
19.	Hermans, S.M.A. Detecting unexplored allosteric pockets to identify novel drug targets Radboud University Nijmegen, The Netherlands, 2015.
18.	Thota, S.S.N.K. Investigation of the thermostability of bacterial laccases based on their 3D structures Rheinische Friedrich-Wilhelms-Universität, Bonn, 2013.
17.	Gertzen, C.G.W. Struktur-Aktivitätsbeziehungen von P2Y11-Antagonisten Christian-Albrechts-Universität, Kiel, 2012.
16.	Sundrashekaran, P. Evaluating the quality of homology models using flexibility conservation within a protein superfamily as a measure. Rheinische Friedrich-Wilhelms-Universität, Bonn, 2010.
15.	Grimme, D. Identifizierung und Charakterisierung krankheitsrelevanter Protein-Komplexe, die sich potentiell für eine Inhibierung durch Helix-Mimetika eignen. Goethe Universität, Frankfurt am Main, 2009.
14.	Dejung, M. Entwicklung eines erweiterbaren Webinterfaces mit Web 2.0 Technologien fur die Binding Interface (BIF) - Datenbank. Goethe Universität, Frankfurt am Main, 2009.
13.	Bergs, J. Entwicklung eines voll-flexiblen Ansatzes zum RNA-Ligand-Docking. Goethe Universität, Frankfurt am Main, 2008.
12.	Krüger, D.M. Evaluierung eines voll-flexiblen Protein-Ligand-Dockingverfahrens. Fachhochschule Oldenburg/Ostfriesland/Wilhelmshaven, Standort Emden, 2007.
11.	Pfleger, C. Untersuchung der Verformbarkeit von Protein-Protien-Epitopen anhand von Computersimulationen. Fachhochschule, Bingen, 2007.
10.	Kopitz, H. Stabilitätsuntersuchungen des Transkriptions-Proteinitiationskomplexes von H. volcanii. Goethe Universität, Frankfurt am Main, 2006.
9.	Metz, A. Entwicklung eines Hybrid-Modells der Solvation für MM-PB/SA Berechnungen. Goethe Universität, Frankfurt am Main, 2006.
8.	Fulle, S. Moleküldynamiksimulationen des ribosomalen Tunnels. Goethe Universität, Frankfurt am Main, 2006.
7.	Wendel, C. Strukturvorhersage von Transmembranhelixpaaren. Goethe Universität, Frankfurt am Main, 2006.
6.	Schmidt, E. Allosterische Regulation durch Rigiditätsperkolation. Goethe Universität, Frankfurt am Main, 2006.
5.	Kazemi, S. Einbeziehung von Rezeptorflexibilität in Protein-Ligand-Dockingverfahren. Goethe Universität, Frankfurt am Main, 2005.
4.	Pfeffer, P. Entwicklung einer Bewertungsfunktion zur Vorhersage von RNA-Ligand-Wechselwirkungen. Goethe Universität, Frankfurt am Main, 2005.
3.	Radestock, S. Molekulardynamiksimulationen zur Untersuchung ungefalteter Proteinzustände. Goethe Universität, Frankfurt am Main, 2005.
2.	Breu, B. Entwicklung einer Consensus-AFMoC-Methode zur Einbeziehung von konformationeller Flexibilität von Rezeptor- und Ligandenstrukturen in Bindeaffinitätsvorhersagen. Fachhochschule, Bingen, 2005.
1.	Ahmed, A. Rigid Cluster Normal Mode Analysis for multi-scale modelling of macromolecular conformational changes. Chalmers University of Technology, Goteborg, Sweden, 2005.