The establishment of the Berlin-Brandenburg research platform BB3R with integrated graduate education will strengthen the 3R expertise of the region Berlin- Brandenburg. Intensive systematic research will provide substantial progress in 3Ralternatives and excellent young scientists will be trained and highly qualified in alternative methods to animal experiments. We have already established a predictive model for the estimation of the expected (in-vitro) estrogenic effect of trace pollutants based on molecular simulation data. We will combine this model with a method for predicting sites of cytochrome P450-mediated hydroxylation in order to extend our estrogene models to the in-vivo situation. In the long run we want to build computer-based models in order to predict special in-vivo effects of small molecules. At least we want to help to prioratize animal testings according to computer-based predictions.

 

Publications

2023
Handlungsempfehlung zur integrativen Bewertung der weitergehenden Abwasserbehandlung von kommunalen Kläranlagen DWA-Themen, Vol.T1/2023, DWA, 2023 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 BibTeX
BB3R - Development, Integration and Continuation of 3R Methods
2021
Neue Medikamente dank Supercomputern Spektrum der Wissenschaft, pp. 40-46, 2021 Konstantin Fackeldey, Christoph Gorgulla, Marcus Weber BibTeX
BB3R - Development, Integration and Continuation of 3R Methods
VirtualFlow Ants—Ultra-Large Virtual Screenings with Artificial Intelligence Driven Docking Algorithm Based on Ant Colony Optimization Special Issue Artificial Intelligence & Deep Learning Approaches for Structural Bioinformatics, 22(11), p. 5807, 2021 Christoph Gorgulla, Süleyman Çınaroğlu, Patrick D. Fischer, Konstantin Fackeldey, Gerhard Wagner, Haribabu Arthanari BibTeX
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BB3R - Development, Integration and Continuation of 3R Methods
2020
Accounting of Receptor Flexibility in Ultra-Large Virtual Screens with VirtualFlow Using a Grey Wolf Optimization Method Supercomputing Frontiers and Innovations, 7(3), pp. 4-12, 2020 Christoph Gorgulla, Konstantin Fackeldey, Gerhard Wagner, Haribabu Arthanari BibTeX
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BB3R - Development, Integration and Continuation of 3R Methods
An open-source drug discovery platform enables ultra-large virtual screens Nature, Vol.580, pp. 663-668, 2020 Christoph Gorgulla, Andras Boeszoermnyi, Zi-Fu Wang, Patrick D. Fischer, Paul Coote, Krishna M. Padmanabha Das, Yehor S. Malets, Dmytro S. Radchenko, Yurii Moroz, David A. Scott, Konstantin Fackeldey, Moritz Hoffmann, Iryna Iavniuk, Gerhard Wagner, Haribabu Arthanari BibTeX
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BB3R - Development, Integration and Continuation of 3R Methods
2019
Computation of temperature-dependent dissociation rates of metastable protein–ligand complexes Molecular Simulation, 45(11), pp. 904-911, 2019 Natalia Ernst, Konstantin Fackeldey, Andrea Volkamer, Oliver Opatz, Marcus Weber BibTeX
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BB3R - Development, Integration and Continuation of 3R Methods
Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung KA Korrespondenz Abwasser, Abfall, Vol.7, pp. 551-557, 2019 Marcus Weber BibTeX
BB3R - Development, Integration and Continuation of 3R Methods
2018
Molecular Binding Kinetics of CYP P450 by Using the Infinitesimal Generator Approach Master's thesis, Technische Universität Berlin, Konstantin Fackeldey, Marcus Weber (Advisors), 2018 Paula Breitbach PDF
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BB3R - Development, Integration and Continuation of 3R Methods
2016
Atomistic Binding Free Energy Estimations for Biological Host–Guest Systems Doctoral thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2016 Vedat Durmaz BibTeX
BB3R - Development, Integration and Continuation of 3R Methods
2015
Computergestützte Simulationen zur Abschätzung gesundheitlicher Risiken durch anthropogene Spurenstoffe der Wassermatrix KA Korrespondenz Abwasser, Abfall, Vol.3/15, pp. 264-267, 2015 Vedat Durmaz, Marcus Weber, Meyer, Mückter BibTeX
BB3R - Development, Integration and Continuation of 3R Methods
2014
Free Energy Simulations of Drug loading for Core-Multishell Nanotransporters J Nanomed Nanotechnol, 5(5), p. 234, 2014 Marcus Weber, Christian Zoschke, Amir Sedighi, Emanuel Fleige, Rainer Haag, Monika Schäfer-Korting BibTeX
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BB3R - Development, Integration and Continuation of 3R Methods
Predicting sites of cytochrome P450-mediated hydroxylation applied to CYP3A4 and hexabromocyclododecane Molecular Simulation, 2014 Olga Scharkoi, Susanne Esslinger, Roland Becker, Marcus Weber, Irene Nehls BibTeX
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BB3R - Development, Integration and Continuation of 3R Methods
2013
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 Vedat Durmaz, Sebastian Schmidt, Peggy Sabri, Christian Piechotta, Marcus Weber PDF
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BB3R - Development, Integration and Continuation of 3R Methods
2012
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 Vedat Durmaz, Marcus Weber, Roland Becker BibTeX
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BB3R - Development, Integration and Continuation of 3R Methods
Östrogenitäts-Approximation mittels physikochemischem Oberflächenvergleich Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2012 Jan-Martin Josten BibTeX
BB3R - Development, Integration and Continuation of 3R Methods