BB3R - Development, Integration and Continuation of 3R Methods
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.
Publikationen
2023 |
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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 |
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2021 |
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Konstantin Fackeldey, Christoph Gorgulla, Marcus Weber | Neue Medikamente dank Supercomputern | Spektrum der Wissenschaft, pp. 40-46, 2021 |
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Christoph Gorgulla, Süleyman Çınaroğlu, Patrick D. Fischer, Konstantin Fackeldey, Gerhard Wagner, Haribabu Arthanari | 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 |
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2020 |
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Christoph Gorgulla, Konstantin Fackeldey, Gerhard Wagner, Haribabu Arthanari | 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 |
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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 | An open-source drug discovery platform enables ultra-large virtual screens | Nature, Vol.580, pp. 663-668, 2020 |
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2019 |
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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 |
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Marcus Weber | Transformationsprodukte im Klärwerk: Mathematische Ansätze der Bewertung | KA Korrespondenz Abwasser, Abfall, Vol.7, pp. 551-557, 2019 |
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2018 |
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Paula Breitbach | Molecular Binding Kinetics of CYP P450 by Using the Infinitesimal Generator Approach | Master's thesis, Technische Universität Berlin, Konstantin Fackeldey, Marcus Weber (Advisors), 2018 |
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2016 |
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Vedat Durmaz | Atomistic Binding Free Energy Estimations for Biological Host–Guest Systems | Doctoral thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2016 |
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2015 |
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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 |
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2014 |
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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 |
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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 |
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2013 |
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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 |
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2012 |
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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 |
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Jan-Martin Josten | Östrogenitäts-Approximation mittels physikochemischem Oberflächenvergleich | Master's thesis, Freie Universität Berlin, Marcus Weber (Advisor), 2012 |
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