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Startseite Research Modeling And Optimization Of Functional Molecules

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.

Modeling and Optimization of Functional Molecules
Group
Computational Molecular Design
Heads
Schütte, Prof. Dr. Christof
Weber, PD Dr. Marcus
Noé , Prof. Dr. Frank
Members
Fackeldey, Priv. Doz. Dr. Konstantin
Partners
FUB (Burkhard Schmidt)
FHI Berlin (Mathias Scheffler)
Funding
DFG

Publications

2018
On Intrinsic Dimension Estimation and Minimal Diffusion Maps Embeddings of Point Clouds Master's thesis, Freie Universität Berlin, Ralf Banisch (Advisor), 2018 Johannes von Lindheim BibTeX
2016
Allosteric and Chelate Cooperativity in Divalent Crown Ether–Ammonium Complexes with Strong Binding Enhancements Chem. Eur. J., 22(43), pp. 15475-15484, 2016 Larissa K. S. Krebek, von, Andreas J. Achazi, Marthe Solleder, Marcus Weber, Beate Paulus, Christoph A. Schalley BibTeX
DOI
2015
Crossing the Scales in Structural Mechanics and Molecular Research Habilitation, Technische Universität Berlin, 2015 Konstantin Fackeldey BibTeX
High affinity flourescence labelled ligands for the estrogen receptor Eur. J. Org. Chem., 2015(10), pp. 2157-2166, 2015 Frank Abendroth, Marthe Solleder, Pia Welker, Kai Licha, Marcus Weber, Oliver Seitz, Dorothea Mangoldt BibTeX
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 Koschek, Vedat Durmaz, Krylova, Wieczorek, Pooja Gupta, Richter, Alexander Bujotzek, Fischer, Rainer Haag, Freund, Marcus Weber, Rademann BibTeX
2014
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) Marcus Weber, Konstantin Fackeldey PDF (ZIB-Report)
BibTeX
DOI
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 Christof Schütte, Peter Deuflhard, Frank Noé, Marcus Weber BibTeX
Local Refinements in Classical Molecular Dynamics Simulations J. Phys. Conf. Ser., Vol.490, p. 012016, 2014 Marcus Weber, Konstantin Fackeldey PDF
BibTeX
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 Marco Sarich, Christof Schütte BibTeX
DOI
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 Peter Deuflhard, Marcus Weber BibTeX
DOI
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) Alexander Bujotzek, Ole Schütt, Adam Nielsen, Konstantin Fackeldey, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI
2013
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) Han Cheng Lie, Konstantin Fackeldey, Marcus Weber PDF (ZIB-Report)
BibTeX
DOI
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 Marcus Weber BibTeX
Adaptive spectral clustering with application to tripeptide conformation analysis The Journal of Chemical Physics, Vol.139, pp. 110-194, 2013 Fiete Haack, Konstantin Fackeldey, Susanna Röblitz, Olga Scharkoi, Marcus Weber, Burkhard Schmidt BibTeX
DOI
Confjump: A method for biomolecular sampling Bachelor's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2013 Remi Toudic BibTeX
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 Susanna Röblitz, Marcus Weber BibTeX
DOI
Konditionsverbesserung von Markov-Modellen Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2013 Daniel Pommer BibTeX
Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches American Mathematical Society, 2013 Christof Schütte, Marco Sarich BibTeX
Molecular Simulation of Multivalent Ligand-Receptor Systems Doctoral thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2013 Alexander Bujotzek BibTeX
On a Generalized Transfer Operator ZIB-Report 13-74 Adam Nielsen, Konstantin Fackeldey, Marcus Weber PDF
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Singulärwertzerlegung mit Zufallsalgorithmen Bachelor's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2013 Jessica Schmiedel BibTeX
2012
A Coarse Graining Method for the Dimension Reduction of the State Space of Biomolecules Journal of Mathematical Chemistry, 5(9), pp. 2623-2635, 2012 Konstantin Fackeldey, Martina Klimm, Marcus Weber BibTeX
A Meshless Method for Conformational Analysis Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2012 Han Cheng Lie BibTeX
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 Konstantin Fackeldey, Alexander Bujotzek, Marcus Weber BibTeX
Free Energy Calculation Using Mayer Cluster Expansion and Fluctuation Free Integration ZIB-Report 12-35 Burcu Tunga, Marcus Weber PDF
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Laufzeitoptimierung der Robusten Perron Cluster Analyse (PCCA+) Master's thesis, Freie Universität Berlin, Susanna Röblitz, Marcus Weber (Advisors), 2012 Mascha Berg PDF
BibTeX
Multiscale Methods in Time and Space Progress in Industrial Mathematics at ECMI 2010, pp. 619-626, Vol.17, Mathematics in Industry, 2012 Konstantin Fackeldey BibTeX
Quantifying the rebinding effect in multivalent chemical ligand-receptor systems J. Chem. Phys., 137(5), p. 054111, 2012 Marcus Weber, Alexander Bujotzek, Rainer Haag BibTeX
The funnel trap paradox ZIB-Report 12-12 Marcus Weber PDF
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2009
Statistical Error Estimation and Grid-free Hierarchical Refinement in Conformation Dynamics Doctoral thesis, Freie Universität Berlin, Peter Deuflhard, Wilhelm Huisinga (Advisors), 2009 Susanna Röblitz PDF
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