Explaining protein ligand complexes with deep learning based scoring functions
Funding: | Sanofi-Aventis Deutschland GmbH |
Runtime: | [05/2023 - 04/2025] |
Staff: | Matthias Rarey |
Verbundprojekt: Röntgenbasierte Medikamenten Entwicklungsplattform
Funding: | BMBF |
Runtime: | [04/2022 - 03/2026] |
Staff: | Thorben Schulze |
Method Development for Synthesis-aware Lead Optimization
Topic: | In the modern drug design process one of the main questions is how to optimize an initial lead compound towards a drug candidate with desired properties. The process of lead optimization is the modification of such an initial lead compound to enhance the desired pharmacological effect and minimize undesirable properties. During this optimization and modification phase, a major challenge is to ensure the synthesizability of the compound. The primary goal of this project is to develop computational strategies to address the problem of synthesis-aware lead optimization. Therefore state-of- the-art techniques, such as combinatorial chemistry and retrosynthetic analysis, are combined. |
Funding: | Bayer AG |
Runtime: | [10/2019 - 09/2022] |
Staff: | Uschi Dolfus |
Partners: | Bayer AG, Universität Hamburg |
GeoMine: Methoden zur geometrischen Mustersuche in Proteinstruktursammlungen
Topic: | Nowadays, more than 150 thousand biomacromolecular structures are available for life science research, a further steep increase can be expected in the next years. This wealth of data can be accessed and queried by all kinds of meta data, searching it by geometric arrangements and features is, however, a widely unsolved problem. Within GeoMine, we are developing database technologies for storing biomacromolecular structural data and quering it with geometrical patterns. |
Funding: | BMBF |
Runtime: | [04/2019 - 03/2022] |
Staff: | Konrad Diedrich, Joel Graef |
Interactive Pocket Exploration and Fragment Growing
Topic: | Goal of the project is to develop computational strategies tackling the problem of fragment growing in a binding pocket, using state of the art computer science methods. Emphasis is placed on the quick response of the developed system that will allow a user to interactively explore their chosen pocket. Eventually the system should also be capable of more advanced functionalities, such as water displacement or macrocyclization. |
Runtime: | [04/2018 - 03/2021] |
Staff: | Patrick Penner |
Partners: | Servier, Universitaet Hamburg (ZBH) |
Allianz protPSI - protein Pressure Specific Activity Impact: Modulation der Reaktivität von Proteinen und Thermodynamik durch Druck
Runtime: | [01/2018 - 12/2020] |
Staff: | Jochen Sieg |
Non-deterministic Search Algorithms for 3D De Novo Design
Topic: | The ZBH has an internationally unique reputation for the development of search methods for chemical fragment spaces. Within this project, a novel pharmacophore-based search engine is developed. Furthermore, novel tools for the analysis and prediction of bioactive conformations are created. |
Funding: | F. Hoffmann-La Roche GmbH |
Runtime: | [07/2007 - 12/2011] |
Staff: | Tobias Lippert, Christin Schärfer |
Partners: | F. Hoffmann-La Roche GmbH, University of Hamburg (ZBH) |
Software: | Qsearch, TorsionAnalyzer |
Paper: |
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Computational Methods for Focussed Library Design
Topic: | A frequent scenario in drug design is the creation of small focused libraries around initial screening hits. For this task, we develop a multi-criteria optimization method for a focused combinatorial library design named LoFT. LoFT considers physico-chemical compound properties as well as similarities and dissimilarities to known compound collections. |
Funding: | Boehringer-Ingelheim |
Runtime: | [11/2006 - 10/2009] |
Staff: | J. Robert Fischer |
Partners: | University of Hamburg (ZBH) |
Software: | LoFT |
Paper: |
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NovoBench: A computational workbench for de novo drug design
Topic: | The aim of Novobench is the development of a toolset for de novo molecular design. The focus of the ZBH work is on the creation of structure-based tools for de novo design (FlexNovo) as well as the combination of de novo design with classical QSAR modeling (FragView and FragEnum). |
Funding: | BMBF (German Ministry of Science and Technology) |
Runtime: | [07/2004 - 06/2008] |
Staff: | Jörg Degen, Juri Pärn |
Partners: | BioSolveIT GmbH, University of Nürnberg-Erlangen, ALTANA Pharma AG, Lilly Forschung GmbH, 4SC AG, Molecular Networks GmbH, University of Hamburg (ZBH) |
Software: | FlexNovo, FragView, FragEnum |
Paper: |
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Ligand-based 3D Scaffold Hopping
Topic: | A frequently occurring scenario is the necessity of redesigning a central part of a lead structure, the core of a molecule. The geometric fit of alterative cores plays a central role in this task. Within this project, we develop a database driven method for fast core replacement under pharmacophoric constraints named Recore, which is widely known and used today. |
Funding: | F. Hoffmann-La Roche GmbH |
Runtime: | [03/2004 - 02/2007] |
Staff: | Patrick Maaß |
Partners: | F. Hoffmann-La Roche GmbH , University of Hamburg (ZBH) |
Link: | http://www.biosolveit.de/recore |
Software: | Recore |
Paper: |
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