Modeling and Optimization of Functional Molecules

In this project we employ function space oriented methods for thermodynamical simulation and analysis of drug-like molecules. Based on a strong mathematical fundament we do cooperative research with other departments from pharmacy, chemistry, medicine and biology. Among these interdisciplinary projects we focus on the development of new and reliable mathematical methods for drug design.

Publikationen

2018 2016 2015 2014 2013 2012 2009

2018
Johannes von Lindheim	On Intrinsic Dimension Estimation and Minimal Diffusion Maps Embeddings of Point Clouds	Master's thesis, Freie Universität Berlin, Ralf Banisch (Advisor), 2018	BibTeX
2016
Larissa K. S. Krebek, von, Andreas J. Achazi, Marthe Solleder, Marcus Weber, Beate Paulus, Christoph A. Schalley	Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements	Chem. Eur. J., 22(43), pp. 15475-15484, 2016	BibTeX DOI
2015
Konstantin Fackeldey	Crossing the Scales in Structural Mechanics and Molecular Research	Habilitation, Technische Universität Berlin, 2015	BibTeX
Frank Abendroth, Marthe Solleder, Pia Welker, Kai Licha, Marcus Weber, Oliver Seitz, Dorothea Mangoldt	High affinity flourescence labelled ligands for the estrogen receptor	Eur. J. Org. Chem., 2015(10), pp. 2157-2166, 2015	BibTeX
Koschek, Vedat Durmaz, Krylova, Wieczorek, Pooja Gupta, Richter, Alexander Bujotzek, Fischer, Rainer Haag, Freund, Marcus Weber, Rademann	Peptide polymer ligands for a tandem WW-domain, a soft multivalent protein-protein interaction: lessons on the thermodynamic fitness of flexible ligands	Beilstein J. Org. Chem., Vol.11, pp. 837-847, 2015	BibTeX
2014
Marcus Weber, Konstantin Fackeldey	Computing the Minimal Rebinding Effect Included in a Given Kinetics	Multiscale Model. Simul., 12(1), pp. 318-334, 2014 (preprint available as ZIB-Report 13-12)	PDF (ZIB-Report) BibTeX DOI
Christof Schütte, Peter Deuflhard, Frank Noé, Marcus Weber	Design of functional molecules	MATHEON-Mathematics for Key Technologies, Vol.1, pp. 49-65, Peter Deuflhard, Martin Grötschel, Dietmar Hömberg, Ulrich Horst, Jürg Kramer, Volker Mehrmann, Konrad Polthier, Frank Schmidt, Christof Schütte, Martin Skutella, Jürgen Sprekels (Eds.), European Mathematical Society, 2014	BibTeX
Marcus Weber, Konstantin Fackeldey	Local Refinements in Classical Molecular Dynamics Simulations	J. Phys. Conf. Ser., Vol.490, p. 012016, 2014	PDF BibTeX
Marco Sarich, Christof Schütte	Markov Model Theory	An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation, Vol.797, pp. 23-44, Gregory R. Bowman, Vijay S. Pande, Frank Noé (Eds.), Springer, 2014	BibTeX DOI
Peter Deuflhard, Marcus Weber	Mathematics without pain	MATHEON-Mathematics for Key Technologies, Vol.1, pp. 26-28, Peter Deuflhard, Martin Grötschel, Dietmar Hömberg, Ulrich Horst, Jürg Kramer, Volker Mehrmann, Konrad Polthier, Frank Schmidt, Martin Skutella, Jürgen Sprekels (Eds.), European Mathematical Society, 2014	BibTeX DOI
Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey, Marcus Weber	ZIBgridfree: Efficient Conformational Analysis by Partition-of-Unity Coupling	Journal of Mathematical Chemistry, 52(3), pp. 781-804, 2014 (preprint available as ZIB-Report 13-58)	PDF (ZIB-Report) BibTeX DOI
2013
Han Cheng Lie, Konstantin Fackeldey, Marcus Weber	A Square Root Approximation of Transition Rates for a Markov State Model	SIAM. J. Matrix Anal. Appl., 34(2), pp. 738-756, 2013 (preprint available as ZIB-Report 13-43)	PDF (ZIB-Report) BibTeX DOI
Marcus Weber	Adaptive Spectral Clustering in Molecular Simulation. In: Studies in Classification, Data Analysis, and Knowledge Organization	XIV: Classification and Data Mining, A. Giusti, G. Ritter, M. Vichi (Eds.), Springer Series, pp. 147-157, 2013	BibTeX
Fiete Haack, Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber, Burkhard Schmidt	Adaptive spectral clustering with application to tripeptide conformation analysis	The Journal of Chemical Physics, Vol.139, pp. 110-194, 2013	BibTeX DOI
Remi Toudic	Confjump: A method for biomolecular sampling	Bachelor's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2013	BibTeX
Susanna Röblitz, Marcus Weber	Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification	Advances in Data Analysis and Classification, 7(2), pp. 147-179, 2013	BibTeX DOI
Daniel Pommer	Konditionsverbesserung von Markov-Modellen	Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2013	BibTeX
Christof Schütte, Marco Sarich	Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches	American Mathematical Society, 2013	BibTeX
Alexander Bujotzek	Molecular Simulation of Multivalent Ligand-Receptor Systems	Doctoral thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2013	BibTeX
Adam Nielsen, Konstantin Fackeldey, Marcus Weber	On a Generalized Transfer Operator	ZIB-Report 13-74	PDF BibTeX URN
Jessica Schmiedel	Singulärwertzerlegung mit Zufallsalgorithmen	Bachelor's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2013	BibTeX
2012
Konstantin Fackeldey, Martina Klimm, Marcus Weber	A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules	Journal of Mathematical Chemistry, 5(9), pp. 2623-2635, 2012	BibTeX
Han Cheng Lie	A Meshless Method for Conformational Analysis	Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2012	BibTeX
Konstantin Fackeldey, Alexander Bujotzek, Marcus Weber	A meshless discretization method for Markov state models applied to explicit water peptide folding simulations	Meshfree Methods for Partial Differential Equations VI, pp. 141-154, Vol.89, Lecture Notes in Computational Science and Engineering, 2012	BibTeX
Burcu Tunga, Marcus Weber	Free Energy Calculation Using Mayer Cluster Expansion and Fluctuation Free Integration	ZIB-Report 12-35	PDF BibTeX URN
Mascha Berg	Laufzeitoptimierung der Robusten Perron Cluster Analyse (PCCA+)	Master's thesis, Freie Universität Berlin, Susanna Röblitz, Marcus Weber (Advisors), 2012	PDF BibTeX
Konstantin Fackeldey	Multiscale Methods in Time and Space	Progress in Industrial Mathematics at ECMI 2010, pp. 619-626, Vol.17, Mathematics in Industry, 2012	BibTeX
Marcus Weber, Alexander Bujotzek, Rainer Haag	Quantifying the rebinding effect in multivalent chemical ligand-receptor systems	J. Chem. Phys., 137(5), p. 054111, 2012	BibTeX
Marcus Weber	The funnel trap paradox	ZIB-Report 12-12	PDF BibTeX URN
2009
Susanna Röblitz	Statistical Error Estimation and Grid-free Hierarchical Refinement in Conformation Dynamics	Doctoral thesis, Freie Universität Berlin, Peter Deuflhard, Wilhelm Huisinga (Advisors), 2009	PDF BibTeX URN