2023
|
| Luca Donati, Konstantin Fackeldey, Marcus Weber |
Augmented ant colony algorithm for virtual drug discovery
|
Journal of Mathematical Chemistry, 2023 (epub ahead of print) |
BibTeX
DOI
|
| Sourav Ray, Konstantin Fackeldey, Christoph Stein, Marcus Weber |
Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane
|
Biophysica, 3(2), pp. 263-275, 2023 |
BibTeX
DOI
|
| Luca Donati, Marcus Weber |
Efficient Estimation of Transition Rates as Functions of pH
|
Proceedings in Applied Mathematics & Mechanics, 2023 (epub ahead of print) |
BibTeX
arXiv
DOI
|
| Thomas Ternes, Karl-Heinz Bauer, Frank Brauer, Jürgen Drewes, Kevin Jewell, Adriano Joss, Jörg Oehlmann, Michael Radtke, Ulrike Schulte-Oehlmann, Thomas Schwartz, Peter Seel, Jeanette Völker, Lilo Weber, Marcus Weber |
Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen
|
DWA-Themen, Vol.T1/2023, DWA, 2023 |
BibTeX
|
| Thomas Ternes, Karl-Heinz Bauer, Frank Brauer, Jörg Drewes, Adriano Joss, Georg Hiller, Kevin Jewell, Jörg Oehlmann, Michael Radke, Ulrike Schulte-Oehlmann, Thomas Schwartz, Peter Seel, Jeanette Völker, Lilo Weber, Marcus Weber |
Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen
|
Christian Wilhelm (Ed.), DWA / GDCh, 2023, ISBN: 978-3-96862-563-8 |
BibTeX
|
| Arne Thies, Vikram Sunkara, Sourav Ray, Hanna Wulkow, M. Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann |
Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design
|
Scientific Reports, 13(607), 2023 |
BibTeX
DOI
|
| Christopher Secker, Konstantin Fackeldey, Marcus Weber, Sourav Ray, Christoph Gorgulla, Christof Schütte |
Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists
|
Journal of Cheminformatics, Vol.15, 2023 |
BibTeX
DOI
|
| Tobias Boege, René Fritze, Christiane Görgen, Jeroen Hanselmann, Dorothea Iglezakis, Lars Kastner, Thomas Koprucki, Tabea Krause, Christoph Lehrenfeld, Silvia Polla, Marco Reidelbach, Christian Riedel, Jens Saak, Björn Schembera, Karsten Tabelow, Marcus Weber |
Research-Data Management Planning in the German Mathematical Community
|
Eur. Math. Soc. Mag., 2023 (epub ahead of print) |
BibTeX
DOI
|
| Surahit Chewle, Marcus Weber, Franziska Emmerling |
Revealing Kinetics of Paracetamol Crystallization Using Time-Resolved Raman Spectroscopy, Orthogonal Time-Lapse Photography, and Non-Negative Matrix Factorization (OSANO)
|
Crystal Growth & Design, 23(9), pp. 6737-6746, 2023 |
BibTeX
DOI
|
| Alexander Sikorski, Amir Niknejad, Marcus Weber, Luca Donati |
Tensor-SqRA: Modeling the Transition Rates of Interacting Molecular Systems in terms of Potential Energies
|
Journal of Chemical Physics, 2023 (under review) |
BibTeX
arXiv
|
2022
|
| Luca Donati, Marcus Weber, Bettina G. Keller |
A review of Girsanov Reweighting and of Square Root Approximation for building molecular Markov State Models
|
Journal of Mathematical Physics, 63(12), pp. 123306-1-123306-21, 2022 |
BibTeX
DOI
|
| Luca Donati, Marcus Weber |
Assessing transition rates as functions of environmental variables
|
The Journal of Chemical Physics, 157(22), pp. 224103-1-224103-14, 2022 |
BibTeX
DOI
|
| Martin Heida, Alexander Sikorski, Marcus Weber |
Consistency and order 1 convergence of cell-centered finite volume discretizations of degenerate elliptic problems in any space dimension
|
SIAM Journal on Numerical Analysis, 2022 (under review) |
BibTeX
DOI
|
| Rita Fernandes, Suvrat Chaowdhary, Noureldin Saleh, Natalia Mikula, Katerina Kanevche, Hans Berlepsch, Naoki Hosogi, Joachim Heberle, Marcus Weber, Christoph Böttcher, Beate Koksch |
Cyanine Dye Coupling Mediates Self-assembly of a pH Sensitive Peptide into Novel 3D Architectures
|
Angewandte Chemie, 61(48), p. e202208647, 2022 |
BibTeX
|
| Peter Benner, Michael Burger, Dominik Göddeke, Christiane Görgen, Christian Himpe, Jan Heiland, Thomas Koprucki, Mario Ohlberger, Stephan Rave, Marco Reidelbach, Jens Saak, Anita Schöbel, Karsten Tabelow, Marcus Weber |
Die mathematische Forschungsdateninitiative in der NFDI: MaRDI (Mathematical Research Data Initiative)
|
GAMM Rundbrief, pp. 40-43, 2022 |
BibTeX
|
| Alexander Sikorski, Enric Ribera Borrell, Marcus Weber |
Learning Koopman eigenfunctions of stochastic diffusions with optimal importance sampling and ISOKANN
|
Journal of Mathematical Physics, 2022 (revision under review) |
BibTeX
arXiv
|
| Marco Reidelbach, Marcus Weber |
MaRDI - The mathematical Research Data Initiative
|
Aktionstag Forschungsdaten, 2022 |
BibTeX
DOI
|
| Franziska Erlekam, Maximilian Zumbansen, Marcus Weber |
Parameter estimation on multivalent ITC data sets
|
Scientific Reports, Vol.12, p. 13402, 2022 |
BibTeX
DOI
|
| N. Alexia Raharinirina, Konstantin Fackeldey, Marcus Weber |
Qualitative Euclidean embedding of Disjoint Sets of Points
|
2022 |
BibTeX
|
| Renata Sechi, Konstantin Fackeldey, Surahit Chewle, Marcus Weber |
SepFree NMF: A Toolbox for Analyzing the Kinetics of Sequential Spectroscopic Data
|
Algorithms, 15(9), p. 297, 2022 |
BibTeX
DOI
|
2021
|
| Konstantin Fackeldey, Jonas Röhm, Amir Niknejad, Surahit Chewle, Marcus Weber |
Analyzing Raman Spectral Data without Separabiliy Assumption
|
Journal of Mathematical Chemistry, 3(59), pp. 575-596, 2021 |
BibTeX
arXiv
DOI
|
| Susanne Röhl, Marcus Weber, Konstantin Fackeldey |
Computing the minimal rebinding effect for non-reversible processes
|
Multiscale Modeling and Simulation, 19(1), pp. 460-477, 2021 |
BibTeX
arXiv
DOI
|
| N. Alexia Raharinirina, Marcus Weber, Ralph Birk, Konstantin Fackeldey, Sarah M. Klasse, Tonio Sebastian Richter |
Different Tools and Results for Correspondence Analysis
|
2021 |
BibTeX
DOI
|
| Renata Sechi, Alexander Sikorski, Marcus Weber |
Estimation of the Koopman Generator by Newton's Extrapolation
|
Multiscale Modeling and Simulation, 19(2), pp. 758-774, 2021 |
BibTeX
DOI
|
| Ralph Birk, N. Alexia Raharinirina, Konstantin Fackeldey, Tonio Sebastian Richter, Marcus Weber |
Inferring cultural and social processes based on patterns of statistical relationships between Synodal texts
|
2021 (in progress) |
BibTeX
|
| Renata Sechi, Marcus Weber, Karsten Heyne |
MSM building and projection for the analysis of time-resolved spectra
|
Proceedings in Applied Mathematics and Mechanics, p. e202100102, 2021 |
BibTeX
DOI
URN
|
| Luca Donati, Marcus Weber, Bettina G. Keller |
Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux
|
Journal of Physics: Condensed Matter, 33(11), p. 115902, 2021 |
BibTeX
DOI
|
| Sourav Ray, Arne Thies, Vikram Sunkara, Hanna Wulkow, Özgür Celik, Fatih Yergöz, Christof Schütte, Christoph Stein, Marcus Weber, Stefanie Winkelmann |
Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design
|
ZIB-Report 21-19 |
PDF
BibTeX
URN
|
| Konstantin Fackeldey, Christoph Gorgulla, Marcus Weber |
Neue Medikamente dank Supercomputern
|
Spektrum der Wissenschaft, pp. 40-46, 2021 |
BibTeX
|
| Wolfgang Bauer, Marcus Weber, Eva Diehl-Wiesenecker, Noa Galtung, Monika Prpic, Rajan Somasundaram, Rudolf Tauber, Jochen Schwenk, Patrick Micke, Kai Kappert |
Plasma Proteome Fingerprints Reveal Distinctiveness and Clinical Outcome of SARS-CoV-2 Infection
|
Viruses, 13(12), p. 2456, 2021 |
BibTeX
DOI
|
| Alexander Sikorski, Marcus Weber, Christof Schütte |
The Augmented Jump Chain
|
Advanced Theory and Simulations, 4(4), 2021 |
BibTeX
arXiv
DOI
|
2020
|
| Marcus Weber, Weitere Autoren |
DIN SPEC 2343: Übertragung von sprachbasierten Daten zwischen Künstlichen Intelligenzen - Festlegung von Parametern und Formaten
|
Beuth Verlag, 2020 |
BibTeX
|
| Surahit Chewle, Franziska Emmerling, Marcus Weber |
Effect of choice of solvent on crystallization pathway of Paracetamol: An experimental and theoretical case study
|
Crystals, 10(12), p. 1107, 2020 |
BibTeX
DOI
|
| Sourav Ray, Vikram Sunkara, Christof Schütte, Marcus Weber |
How to calculate pH-dependent binding rates for receptor-ligand systems based on thermodynamic simulations with different binding motifs
|
Molecular Simulation, 46(18), pp. 1443-1452, 2020 (preprint available as ZIB-Report 20-18) |
PDF (ZIB-Report)
BibTeX
DOI
|
| Robert Julian Rabben, Sourav Ray, Marcus Weber |
ISOKANN: Invariant subspaces of Koopman operators learned by a neural network
|
The Journal of Chemical Physics, 153(11), p. 114109, 2020 |
BibTeX
DOI
|
| José Villatoro, Martin Zühlke, Daniel Riebe, Toralf Beitz, Marcus Weber, Hans-Gerd Löhmannsröben |
Sub-ambient pressure IR-MALDI ion mobility spectrometer for the determination of low and high field mobilities
|
Analytical and Bioanalytical Chemistry, Vol.412, pp. 5247-5260, 2020 |
BibTeX
DOI
|
2019
|
| Natalia Ernst, Konstantin Fackeldey, Andrea Volkamer, Oliver Opatz, Marcus Weber |
Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes
|
Molecular Simulation, 45(11), pp. 904-911, 2019 |
BibTeX
DOI
|
| Konstantin Fackeldey, Peter Koltai, Peter Nevir, Henning Rust, Axel Schild, Marcus Weber |
From metastable to coherent sets - Time-discretization schemes
|
Chaos: An Interdisciplinary Journal of Nonlinear Science, Vol.29, pp. 012101-012101, 2019 (preprint available as ZIB-Report 17-74) |
PDF (ZIB-Report)
BibTeX
DOI
|
| Bernhard Reuter, Konstantin Fackeldey, Marcus Weber |
Generalized Markov modeling of nonreversible molecular kinetics
|
The Journal of Chemical Physics, 17(150), p. 174103, 2019 |
BibTeX
DOI
|
| Franziska Erlekam, Sinaida Igde, Susanna Röblitz, Laura Hartmann, Marcus Weber |
Modeling of Multivalent Ligand-Receptor Binding Measured by kinITC
|
Computation, 7(3), p. 46, 2019 |
BibTeX
DOI
|
| Narendra Lagumaddepalli Venkatareddy, Patrick Wilke, Natalia Ernst, Justus Horch, Marcus Weber, Andre Dallmann, Hans G. Börner |
Mussel-glue inspired adhesives: A study on the relevance of L-Dopa and the function of the sequence at nanomaterial-peptide interfaces
|
Advanced Materials Interfaces, 6(13), p. 1900501, 2019 |
BibTeX
DOI
|
| José Villatoro, Marcus Weber, Martin Zühlke, Andreas Lehmann, Karl Zechiowski, Daniel Riebe, Toralf Beitz, Hans-Gerd Löhmannsröben, Oliver Kreuzer |
Structural characterization of synthetic peptides using electronspray ion mobility spectrometry and molecular dynamics simulations
|
International Journal of Mass Spectrometry, Vol.436, pp. 108-117, 2019 |
BibTeX
DOI
|
|
Marcus Weber
|
Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung
|
KA Korrespondenz Abwasser, Abfall, Vol.7, pp. 551-557, 2019 |
BibTeX
|
| Aennes Abbas, Ilona Schneider, Anna Bollmann, Jan Funke, Jörg Oehlmann, Carsten Prasse, Ulrike Schulte-Oehlmann, Wolfram Seitz, Thomas Ternes, Marcus Weber, Henning Wesely, Martin Wagner |
What you extract is what you see: Optimising the preparation of water and wastewater samples for in vitro bioassays
|
Water Research, Vol.152, pp. 47-60, 2019 |
BibTeX
DOI
|
| Giovanna Del Vecchio, Dominika Labuz, Julia Temp, Viola Seitz, Michael Kloner, Roger Negrete, Antonio Rodriguez-Gaztelumendi, Marcus Weber, Halina Machelska, Christoph Stein |
pKa of opioid ligands as a discriminating factor for side effects
|
Scientific Reports, Vol.9, p. 19344, 2019 |
BibTeX
DOI
|
2018
|
| Katharina Schrade, Jessica Tröger, Adeep Eldashan, Kerstin Zühlke, Kamal R. Abdul Azees, Jonathan M. Elkins, Martin Neuenschwander, Andreas Oder, Mohamed Elkewedi, Sarah Jaksch, Karsten Andrae, Jinliang Li, Jaoa Fernandes, Paul Markus Müller, Stephan Grunwald, Stephen F. Marino, Tanja Vukicevic, Jenny Eichhorst, Burkhard Wiesner, Marcus Weber, Michael Kapiloff, Oliver Rocks, Oliver Daumke, Thomas Wieland, Stefan Knapp, Jens Peter von Kries, Enno Klussmann |
An AKAP-Lbc-RhoA interaction inhibitor promotes the translocation of aquaporin-2 to the plasma membrane of renal collecting duct principal cells
|
PLOS ONE, 13(1), pp. e0191423-e0191423, 2018 |
BibTeX
DOI
|
| Jannes Quer, Luca Donati, Bettina Keller, Marcus Weber |
An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates
|
SIAM Journal on Scientific Computing, 40(2), pp. A653-A670, 2018 (preprint available as ZIB-Report 17-09) |
PDF (ZIB-Report)
BibTeX
DOI
|
| Luca Donati, Martin Heida, Bettina G. Keller, Marcus Weber |
Estimation of the infinitesimal generator by square-root approximation
|
J. Phys.: Condens. Matter, 30(42), pp. 425201-425201, 2018 |
BibTeX
DOI
|
| Bernhard Reuter, Marcus Weber, Konstantin Fackeldey, Susanna Röblitz, Martin E. Garcia |
Generalized Markov State Modeling Method for Nonequilibrium Biomolecular Dynamics: Exemplified on Amyloid β Conformational Dynamics Driven by an Oscillating Electric Field
|
Journal of Chemical Theory and Computation, 14(7), pp. 3579-3594, 2018 |
BibTeX
DOI
|
|
Marcus Weber
|
Implications of PCCA+ in Molecular Simulation
|
Computation, 6(1), p. 20, 2018 |
BibTeX
DOI
|
| Natasa Djurdjevac Conrad, Daniel Fuerstenau, Ana Grabundzija, Luzie Helfmann, Martin Park, Wolfram Schier, Brigitta Schütt, Christof Schütte, Marcus Weber, Niklas Wulkow, Johannes Zonker |
Mathematical modeling of the spreading of innovations in the ancient world
|
eTopoi. Journal for Ancient Studies, Vol.7, 2018 |
PDF
BibTeX
DOI
|
| Jakob Witzig, Isabel Beckenbach, Leon Eifler, Konstantin Fackeldey, Ambros Gleixner, Andreas Grever, Marcus Weber |
Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes
|
Multiscale Modeling and Simulation, 16(1), pp. 248-265, 2018 (preprint available as ZIB-Report 16-39) |
PDF (ZIB-Report)
BibTeX
DOI
|
| Viola Spahn, Giovanna Del Vecchio, Antonio Rodriguez-Gaztelumendi, Julia Temp, Dominika Labuz, Michael Kloner, Marco Reidelbach, Halina Machelska, Marcus Weber, Christoph Stein |
Opioid receptor signaling, analgesic and side effects induced by a computationally designed pH-dependent agonist
|
Scientific Reports, Vol.8, p. 8965, 2018 |
BibTeX
|
| Marco Reidelbach, Marcus Weber, Petra Imhof |
Prediction of perturbed proton transfer networks
|
PLoS ONE, 13(12), pp. e0207718-e0207718, 2018 |
BibTeX
DOI
|
| Sabine Wagner, Carlos Zapata, Wei Wan, Kornelia Gawlitza, Marcus Weber, Knut Rurack |
Role of Counterions in Molecularly Imprinted Polymers for Anionic Species
|
Langmuir, 34(23), pp. 6963-6975, 2018 |
BibTeX
DOI
|
| Konstantin Fackeldey, Alexander Sikorski, Marcus Weber |
Spectral Clustering for Non-Reversible Markov Chains
|
Computational and Applied Mathematics, 37(5), pp. 6376-6391, 2018 (preprint available as ZIB-Report 18-48) |
PDF (ZIB-Report)
BibTeX
DOI
|
|
Marcus Weber
|
Supplementary: Implications of PCCA+ in Molecular Simulation
|
2018 |
BibTeX
|
|
Marcus Weber
|
Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung
|
KA Korrespondenz Abwasser, Abfall, 2018 (accepted for publication) |
BibTeX
|
2017
|
| Viola Spahn, Giovanna Del Vecchio, Dominika Labuz, Antonio Rodriguez-Gaztelumendi, N. Massaly, Julia Temp, Vedat Durmaz, P. Sabri, Marco Reidelbach, Halina Machelska, Marcus Weber, Christoph Stein |
A nontoxic pain killer designed by modeling of pathological receptor conformations
|
Science, 355(6328), pp. 966-969, 2017 |
BibTeX
DOI
|
|
Marcus Weber
|
Eigenvalues of non-reversible Markov chains – A case study
|
ZIB-Report 17-13 |
PDF
BibTeX
URN
|
| Konstantin Fackeldey, Amir Niknejad, Marcus Weber |
Finding Metastabilities in Reversible Markov Chains based on Incomplete Sampling: Case of Molecular Simulation
|
Special Matrices, pp. 73-81, 2017 |
BibTeX
DOI
|
| Konstantin Fackeldey, Marcus Weber |
GenPCCA -- Markov State Models for Non-Equilibrium Steady States
|
Big data clustering: Data preprocessing, variable selection, and dimension reduction. WIAS Report No. 29, pp. 70-80, 2017 |
BibTeX
DOI
|
| Carsten Hartmann, Christof Schütte, Marcus Weber, Wei Zhang |
Importance sampling in path space for diffusion processes with slow-fast variables
|
Probability Theory and Related Fields, pp. 1-52, 2017 |
BibTeX
DOI
|
| Sinaida Igde, Susanna Röblitz, Anne Müller, Katharina Kolbe, Sophia Boden, Claudia Fessele, Thisbe Lindhorst, Marcus Weber, Laura Hartmann |
Linear Precision Glycomacromolecules with Varying Interligand Spacing and Linker Functionalities Binding to Concanavalin A and the Bacterial Lectin FimH
|
Marcomolecular Bioscience, 17(12), p. 1700198, 2017 |
BibTeX
DOI
|
| Marcus Weber, Konstantin Fackeldey, Christof Schütte |
Set-Free Markov State Model Building
|
Journal of Chemical Physics, 146(12), 2017 (preprint available as ZIB-Report 17-10) |
PDF (ZIB-Report)
BibTeX
DOI
|
| Marcus Weber, Vedat Durmaz, Peggy Sabri, Marco Reidelbach |
Supplementary simulation data for Science Manuscript ai8636
|
2017 |
BibTeX
DOI
|
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
|
| Natasa Djurdjevac Conrad, Marcus Weber, Christof Schütte |
Finding dominant structures of nonreversible Markov processes
|
Multiscale Modeling and Simulation, 14(4), pp. 1319-1340, 2016 (preprint available as ZIB-Report 15-40) |
PDF (ZIB-Report)
BibTeX
DOI
|
| José Villatoro, Martin Zühlke, Daniel Riebe, Toralf Beitz, Marcus Weber, Jens Riedel, Hans-Gerd Löhmannsröben |
IR-MALDI ion mobility spectrometry: physical source characterization and application as HPLC detector
|
International Journal for Ion Mobility Spectrometry, pp. 197-297, 2016 |
BibTeX
DOI
|
2015
|
| Vedat Durmaz, Marcus Weber, Meyer, Mückter |
Computergestützte Simulationen zur Abschätzung gesundheitlicher Risiken durch anthropogene Spurenstoffe der Wassermatrix
|
KA Korrespondenz Abwasser, Abfall, Vol.3/15, pp. 264-267, 2015 |
BibTeX
|
| Adam Nielsen, Marcus Weber |
Computing the nearest reversible Markov chain
|
Numerical Linear Algebra with Applications, 22(3), pp. 483-499, 2015 (preprint available as ZIB-Report 14-48) |
PDF (ZIB-Report)
BibTeX
DOI
|
| Marcus Weber, Jannes Quer |
Estimating exit rates in rare event dynamical systems via extrapolation
|
ZIB-Report 15-54 |
PDF
PDF
BibTeX
URN
|
| Marcus Weber, Konstantin Fackeldey |
G-PCCA: Spectral Clustering for Non-reversible Markov Chains
|
ZIB-Report 15-35 |
PDF
BibTeX
URN
|
| 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
|
| Sinaida Igde, Hendrik Wölk, Susanna Röblitz, Marco Reidelbach, Marcus Weber, Laura Hartmann |
Identifying Multivalent Binding Kinetics of Precision Glycomacromolecules: A Kinetic Study Using kinITC
|
Münster Symposium on Cooperative Effects 2015 - SFB 858, at Westfälische Wilhelms-Universität Münster, 2015, 2015 |
BibTeX
|
| Christof Schütte, Adam Nielsen, Marcus Weber |
Markov State Models and Molecular Alchemy
|
Molecular Physics, 113(1), pp. 69-78, 2015 (preprint available as ZIB-Report 14-05) |
PDF (ZIB-Report)
BibTeX
DOI
|
| 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
|
| Wei Zhang, Han Wang, Carsten Hartmann, Marcus Weber, Christof Schütte |
Applications of the cross-entropy method to importance sampling and optimal control of diffusions
|
Siam Journal on Scientific Computing, 36(6), pp. A2654-A2672, 2014 (preprint available as ZIB-Report 14-10) |
PDF (ZIB-Report)
BibTeX
DOI
|
| 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, Christian Zoschke, Amir Sedighi, Emanuel Fleige, Rainer Haag, Monika Schäfer-Korting |
Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters
|
J Nanomed Nanotechnol, 5(5), p. 234, 2014 |
BibTeX
DOI
|
| Karsten Andrae, Stefan Merkel, Vedat Durmaz, Konstantin Fackeldey, Robert Köppen, Marcus Weber, Matthias Koch |
Investigation of the Ergopeptide Epimerization Process
|
Computation, 2(3), pp. 102-111, 2014 |
BibTeX
DOI
|
| Marcus Weber, Konstantin Fackeldey |
Local Refinements in Classical Molecular Dynamics Simulations
|
J. Phys. Conf. Ser., Vol.490, p. 012016, 2014 |
PDF
BibTeX
|
| 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
|
| Olga Scharkoi, Susanne Esslinger, Roland Becker, Marcus Weber, Irene Nehls |
Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane
|
Molecular Simulation, 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
|
| Vedat Durmaz, Sebastian Schmidt, Peggy Sabri, Christian Piechotta, Marcus Weber |
A hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens
|
Journal of Chemical Information and Modeling, 53(10), pp. 2681-2688, 2013 |
PDF
BibTeX
|
|
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
|
| Olga Scharkoi, Konstantin Fackeldey, Igor Merkulow, Karsten Andrae, Marcus Weber, Irene Nehls |
Conformational Analysis of Alternariol on the Quantum Level
|
J. Mol. Model., 19(6), pp. 2567-2572, 2013 |
BibTeX
DOI
|
| Christoph Stein, Marcus Weber, Christian Zöllner, Olga Scharkoi |
Fentanyl derivatives as pH-dependent opioid receptor agonists
|
European Patent Application, Bulletin 2013/08, 2013 |
PDF
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
|
| Rahul Tyagi, Shashwat Malhotra, Andreas F. Thünemann, Amir Sedighi, Marcus Weber, Andreas Schäfer, Rainer Haag |
Investigations of Host-Guest Interactions with Shape-persistent Nonionic Dendritic Micelles
|
J. Phys. Chem. C, 117(23), pp. 12307-12317, 2013 |
BibTeX
|
| Karsten Andrae, Vedat Durmaz, Konstantin Fackeldey, Olga Scharkoi, Marcus Weber |
Medizin aus dem Computer
|
Der Anaesthesist, 62(7), pp. 561-557, 2013 |
BibTeX
DOI
|
| Christoph Stein, Marcus Weber, Olga Scharkoi, Peter Deuflhard |
Method and system for identifying compounds that bind and preferably activate a target opioid receptor in a pH-dependent manner
|
European Patent Application, Bulletin 2013/28, 2013 |
PDF
BibTeX
|
| Min Shan, Kathryn E. Carlson, Alexander Bujotzek, Anja Wellner, Ronald Gust, Marcus Weber, John A. Katzenellenbogen, Rainer Haag |
Nonsteroidal Bivalent Estrogen Ligands - An Application of the Bivalent Concept to the Estrogen Receptor
|
ACS Chem. Biol., 8(4), pp. 707-715, 2013 |
PDF
BibTeX
|
| Adam Nielsen, Konstantin Fackeldey, Marcus Weber |
On a Generalized Transfer Operator
|
ZIB-Report 13-74 |
PDF
BibTeX
URN
|
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
|
| 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
|
| Vedat Durmaz, Marcus Weber, Roland Becker |
How to Simulate Affinities for Host-Guest Systems Lacking Binding Mode Information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers
|
Journal of Molecular Modeling, Vol.18, pp. 2399-2408, 2012 |
BibTeX
DOI
|
| Carlo Fasting, Christoph A. Schalley, Marcus Weber, Oliver Seitz, Stefan Hecht, Beate Koksch, Jens Dernedde, Christina Graf, Ernst-Walter Knapp, Rainer Haag |
Multivalency as a Chemical Organization and Action Principle
|
Angew. Chem. Int. Ed., 51(42), pp. 10472-10498, 2012 |
BibTeX
|
| Robert Köppen, Juliane Riedel, Matthias Proske, Sarah Drzymala, Tatjana Rasenko, Vedat Durmaz, Marcus Weber, Matthias Koch |
Photochemical trans-/cis-isomerization and quantification of zearalenone in edible oils
|
J. Agric. Food Chem., Vol.60, pp. 11733-11740, 2012 |
BibTeX
DOI
|
| 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
|
2011
|
|
Marcus Weber
|
A Subspace Approach to Molecular Markov State Models via a New Infinitesimal Generator
|
Habilitation, Freie Universität Berlin, 2011 |
PDF
PDF
PDF
BibTeX
URN
|
| Vedat Durmaz, Konstantin Fackeldey, Marcus Weber |
A rapidly Mixing Monte Carlo Method for the Simulation of Slow Molecular Processes
|
Applications of Monte Carlo Methods in Biology, Medicine and Other Fields of Science, Ch. Mode (Ed.), InTech, 2011 |
BibTeX
|
| Marcus Weber, Alexander Bujotzek, Karsten Andrae, M. Weinhart, Rainer Haag |
Computational entropy estimation of linear polyether modified surfaces and correlation with protein resistant properties of such surfaces
|
J. Mol. Sim., 2011 |
BibTeX
|
| Min Shan, Alexander Bujotzek, Frank Abendroth, Oliver Seitz, Marcus Weber, Rainer Haag |
Conformational Analysis of Bivalent Estrogen Receptor-Ligands: From Intramolecular to Intermolecular Binding
|
ChemBioChem, 12(17), pp. 2587-2598, 2011 |
BibTeX
DOI
|
| Frank Abendroth, Alexander Bujotzek, Min Shan, Rainer Haag, Marcus Weber, Oliver Seitz |
DNA-controlled bivalent presentation of ligands for the estrogen receptor
|
Angew. Chem. Int. Ed., 2011 |
BibTeX
|
| Ch. Scheibe, Alexander Bujotzek, Jens Dernedde, Marcus Weber, O. Seitz |
DNA-programmed spatial screening of carbohydrate-lectin interactions
|
Chem. Sci., Vol.2, pp. 770-775, 2011 |
BibTeX
|
| Martina Klimm, Alexander Bujotzek, Marcus Weber |
Direct Reweighting Strategies in Conformation Dynamics
|
MATCH Commun. Math. Comp. Chem., Vol.65(2), pp. 333-346, 2011 |
BibTeX
|
| O. Scharkoi, Susanne Esslinger, Roland Becker, Marcus Weber, Irene Nehls |
Phase I oxidation of alpha- and gamma-hexabromocyclododecane by cytochrome P450 enzymes: simulation of the stereoisomerism of hydroxylated metabolites
|
Organohalogen Compounds, Vol.73, pp. 730-733, 2011 |
PDF
BibTeX
|
| Konstantin Fackeldey, Susanna Röblitz, O. Scharkoi, Marcus Weber |
Soft Versus Hard Metastable Conformations in Molecular Simulations
|
Particle Methods II, Fundamentals and Applications, Barcelona, Spain 26-28 Oct. 2011, E. Onate and D.R.J. Owen (eds.), pp. 899-909, 2011 (preprint available as ZIB-Report 11-27) |
PDF (ZIB-Report)
BibTeX
|
| Alexander Bujotzek, Min Shan, Rainer Haag, Marcus Weber |
Towards a rational spacer design for bivalent inhibition of estrogen receptor
|
J. Comput.-Aided Mol. Des., Vol.25(3), pp. 253-262, 2011 |
BibTeX
|
2010
|
| Marcus Weber, Karsten Andrae |
A simple method for the estimation of entropy differences
|
MATCH Commun. Math. Comp. Chem. 2010, Vol.63(2), pp. 319-332, 2010 |
BibTeX
|
| Fiete Haack, Susanna Röblitz, Olga Scharkoi, Burkhard Schmidt, Marcus Weber |
Adaptive Spectral Clustering for Conformation Analysis
|
AIP Conference Proceedings, 1281(1), pp. 1585-1588, 2010 |
BibTeX
DOI
|
| D. Siegel, Karsten Andrae, Matthias Proske, C. Kochan, Matthias Koch, Marcus Weber, Irene Nehls |
Dynamic covalent hydrazine chemistry as a specific extraction and cleanup technique for the quantification of the Fusarium mycotoxin zearalenone in edible oils
|
Journal of Chromatography A, Vol.1217(15), pp. 2206-15, 2010 |
BibTeX
|
| H. H. Dieter, K. Götz, K. Kümmerer, B. Rechenberg, F. Keil |
Handlungsmöglichkeiten zur Minderung des Eintrags von Humanarzneimitteln und ihren Rückständen in das Roh- und Trinkwasser.
|
H.H. Dieter, K. Götz, K. Kümmerer, B. Rechenberg, F. Keil (Eds.), Umweltbundesamt, 2010 |
PDF
BibTeX
|
| Ph. Metzner, Marcus Weber, Christof Schütte |
Observation uncertainty in reversible Markov chains
|
Phys. Rev. E, 82(3), p. 031114, 2010 |
BibTeX
DOI
|
2009
|
|
Marcus Weber
|
A Subspace Approach to Molecular Markov State Models via an Infinitesimal Generator
|
ZIB-Report 09-27 |
PDF
PDF
BibTeX
URN
|
| Alexander Bujotzek, Marcus Weber |
Efficient Simulation of Ligand-Receptor Binding Processes Using the Conformation Dynamics Approach
|
Journal of Bioinformatics and Computational Biology, Vol.7(5), pp. 811-831, 2009 |
BibTeX
|
| Susanna Röblitz, Marcus Weber |
Fuzzy Spectral Clustering by PCCA+
|
Classification and Clustering: Models, Software and Applications, pp. 73-79, 2009 |
BibTeX
|
| Robert Köppen, Roland Becker, Marcus Weber, Vedat Durmaz, Irene Nehls |
HBCD stereoisimers: Thermal interconversion and enantiospecific trace analysis in biota
|
Organohalogen Compounds, Vol.70, pp. 910-913, 2009 |
BibTeX
|
| Marcus Weber, Vedat Durmaz, Roland Becker, Susanne Esslinger |
Predictive Identification of Pentabromocyclododecane (PBCD) Isomers with high Binding Affinity to hTTR
|
Organohalogen Compounds, Vol.71, pp. 247-252, 2009 |
BibTeX
|
|
Marcus Weber
|
Spurenstoffe im Trinkwasser - Risikoqualifizierung im Rechner?
|
Schriftenreihe des Vereins für Wasser-, Boden- und Lufthygiene, L. Dunemann, O. Schmoll (Eds.), 2009 |
BibTeX
|
2008
|
|
Marcus Weber
|
An efficient analysis of rare events in canonical ensemble dynamics
|
ZIB-Report 08-36 |
PDF
BibTeX
URN
|
| Marcus Weber, Roland Becker, Robert Köppen, Vedat Durmaz |
Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane
|
Journal of Molecular Simulation, 34(7), pp. 727-736, 2008 (preprint available as ZIB-Report 07-31) |
PDF (ZIB-Report)
BibTeX
|
| Susanna Kube, Marcus Weber |
Computation of equilibrium densities in metastable dynamical systems by domain decomposition
|
Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008, pp. 339-342, Vol.1048, 2008 |
BibTeX
|
| Susanna Kube, Caroline Lasser, Marcus Weber |
Monte Carlo sampling of Wigner functions and surface hopping quantum dynamics
|
Journal of Computational Physics, 228(6), pp. 1947-1962, 2008 (preprint available as ZIB-Report 07-17) |
PDF (ZIB-Report)
BibTeX
DOI
|
| Susanna Kube, Marcus Weber |
Preserving the Markov Property of Reduced Reversible Markov Chains
|
Numerical Analysis and Applied Mathematics, International Conference on Numerical Analysis and Applied Mathematics 2008, pp. 593-596, Vol.1048, 2008 |
BibTeX
|
| A. Guerler, Sebastian Moll, Marcus Weber, Holger Meyer, Frank Cordes |
Selection and flexible optimization of binding modes from conformation ensembles
|
Biosystems, 92(1), pp. 42-48, 2008 |
BibTeX
DOI
|
2007
|
| Susanna Kube, Marcus Weber |
A Coarse Graining Method for the Identification of Transition rates between Molecular Conformations
|
Journal of Chemical Physics, 126(2), 2007 |
BibTeX
DOI
|
|
Marcus Weber
|
Conformation-based transition state theory
|
ZIB-Report 07-18 |
PDF
BibTeX
URN
|
| A. Gürler, Sebastian Moll, Marcus Weber, Holger Meyer, Frank Cordes |
Selection and flexible optimization of binding modes from conformation ensembles
|
Biosystems, 2007 |
BibTeX
|
| Marcus Weber, Susanna Kube, Lionel Walter, Peter Deuflhard |
Stable Computation of Probability Densities of Metastable Dynamical Systems
|
SIAM J. Multiscale Model. Simul., 6(2), pp. 396-416, 2007 |
BibTeX
|
| C. Förster, Arnd B. E. Brauer, J. Fürste, C. Betzel, Marcus Weber, Frank Cordes, V. Erdmann |
Visualization of the tRNA(Ser) acceptor step binding site in the seryl-tRNA synthetase
|
BBRC, 362(2), pp. 415-418, 2007 |
BibTeX
|
| R. Kellermann, Marcus Weber, Alexander Bujotzek |
Vom Dietrich zum Sicherheitsschlüssel – Mathematiker des Matheon simulieren neuen Wirkstoff für die Diabetes-Behandlung
|
DFG-Forschungszentrum Matheon, 2007 |
BibTeX
|
2006
|
| Marcus Weber, Wasinee Rungsarityotin, Alexander Schliep |
An Indicator for the Number of Clusters
|
From Data and Information Analysis to Knowledge Engineering, Myra Spiliopoulou, Rudolf Kruse, Christian Borgelt, Andreas Nürnberger, Wolfgang Gaul (Eds.), Springer Berlin Heidelberg, pp. 103-110, 2006 |
BibTeX
|
| Susanna Kube, Marcus Weber |
Coarse Grained Molecular Kinetics
|
ZIB-Report 06-35 (Appeared as : "A coarse grained method for the identification of transition rates between molecular conformations" in Journal of Chemical Physics, 126(2) 2007) |
PDF
BibTeX
URN
|
| Holger Meyer, Sebastian Moll, Frank Cordes, Marcus Weber |
ConFlow? A new space-based Application for complete Conformational Analysis of Molecules
|
ZIB-Report 06-31 |
PDF
BibTeX
URN
|
| Lionel Walter, Marcus Weber |
ConfJump : a fast biomolecular sampling method which drills tunnels through high mountains
|
ZIB-Report 06-26 |
PDF
BibTeX
URN
|
| Marcus Weber, Susanna Kube, Alexander Riemer, Alexander Bujotzek |
Efficient Sampling of the Stationary Distribution of Metastable Dynamical Systems
|
ZIB-Report 07-03 |
PDF
BibTeX
URN
|
|
Marcus Weber
|
Meshless Methods in Confirmation Dynamics
|
Doctoral thesis, Freie Universität Berlin, Peter Deuflhard, M. Dellnitz (Advisors), 2006 |
PDF
BibTeX
URN
|
|
Marcus Weber
|
Meshless Methods in Conformation Dynamics
|
Doctoral thesis, Freie Universität Berlin, department of mathematics, 2006 |
BibTeX
|
| Marcus Weber, Lionel Walter, Susanna Kube, Peter Deuflhard |
Stable computation of probability densities for metastable dynamical systems
|
ZIB-Report 06-39 (Appeared in: SIAM J. Multisc. Mod. Sim. 2007, 6(2), pp. 396-416) |
PDF
BibTeX
URN
|
2005
|
| Susanna Kube, Marcus Weber |
Conformation Kinetics as a Reduced Model for Transition Pathways
|
ZIB-Report 05-43 |
PDF
BibTeX
URN
|
| Susanna Kube, Marcus Weber |
Identification of Metastabilities in Monomolecular Conformation Kinetics
|
ZIB-Report 06-01 |
PDF
BibTeX
URN
|
| Marcus Weber, Susanna Kube |
Robust Perron Cluster Analysis for Various Applications in Computational Life Science
|
Computational Life Sciences, pp. 57-66, 2005 |
BibTeX
|
| Peter Deuflhard, Marcus Weber |
Robust Perron Cluster Analysis in Conformation Dynamics
|
Lin. Alg. Appl. – Special Issue on Matrices and Mathematical Biology, Elsevier Journals: Germany, pp. 161-184, 2005 (preprint available as ZIB-Report 03-19) |
PDF (ZIB-Report)
PDF (ZIB-Report)
BibTeX
|
| Marcus Weber, Holger Meyer |
ZIBgridfree - Adaptive Conformation Analysis with qualified Support of Transition States and Thermodynamic Weights
|
ZIB-Report 05-17 |
PDF
BibTeX
URN
|
2004
|
| Marcus Weber, Wasinee Rungsarityotin, Alexander Schliep |
Perron Cluster Analysis and Its Connection to Graph Partitioning for Noisy Data
|
ZIB-Report 04-39 |
PDF
BibTeX
URN
|
2003
|
|
Marcus Weber
|
Clustering by using a simplex structure
|
ZIB-Report 04-03 |
PDF
BibTeX
URN
|
|
Marcus Weber
|
Improved Perron Cluster Analysis
|
ZIB-Report 03-04 |
PDF
BibTeX
URN
|
2002
|
| Marcus Weber, Tobias Galliat |
Characterization of Transition States in Conformational Dynamics using Fuzzy Sets
|
ZIB-Report 02-12 |
PDF
BibTeX
URN
|
| Frank Cordes, Marcus Weber, Johannes Schmidt-Ehrenberg |
Metastable Conformations via successive Perron-Cluster Cluster Analysis of dihedrals
|
ZIB-Report 02-40 |
PDF
BibTeX
URN
|
zib.de