Team Volkamer - in silico toxicology and structural bioinformatics

The group of JProf. Volkamer is working on novel methods for in-silico toxicology predictions.

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The project is part of the BMBF-funded BB3R initiative. One major goal of the BB3R initiative is the establishment of alternative methods for preclinical drug development and basic research. To assess the toxicity of novel chemical entities, regulatory agencies require in-vivo testing for several toxic endpoints. In 2010, roughly 2.9 million laboratory animals have been deployed in Germany, with an increase of 6% since 2008. Thus, the establishment of alternative methods, and with it the reduction of animal testing, is of utmost importance. Determining the toxicity of compounds is vital to identify their harmful effects on humans, animals, plants and the environment.

The focus of the AG Volkamer is the development of structure-based methods to come closer to the vision of transforming toxicology into a predictive science and reducing the number of animal testing. The group strongly focuses on computer-aided prediction of off-target effects as well as the identification of novel 'toxicophores' and toxicity targets (targets associated with adverse drug reactions) using ligand- as well as protein-based structural and physicochemical information. 

Structure-based (binding site assessment and comparison, pharmacophore elucidation, structure-function relationship) and ligand-based (screening, QSAR, machine learning) methods are investigated to guide the design of more selective and less toxic compounds.

The group is looking forward to new challenges and new collaborations with computational and experimental partners to jointly apply the novel methods to acute questions.

Publications / Awards

  • Mortier, Dhakal, Volkamer, (2018). Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces, Molecules, 23(8), 1959
  • Volkamer, Riniker, (2018). Transition from Academia to Industry and Back, J. Chem. Inf. Model.
  • Volkamer, et al., (2018). Prediction, Analysis and Comparison of Active Sites; Book chapter in Cheminformatics, Basic Concepts and methods (Wiley), ed. Engel, Gasteiger
  • Lang, Volkamer, et al., (2018). In silico Methods – Computational Alternatives to Animal Testing. ALTEX - Alternatives to animal experimentation. 35(1): 126-128.
  • Kooistra, Volkamer, (2017). Kinase-centric computational drug development. Book chapter: Annual Reports in Medicinal Chemistry (Elsevier): Platform Technologies in Drug Discovery and Target Validation, Volume 50, 197-236.
  • Bietz, et al., Volkamer, Rarey, (2017). From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library. J.Biotec., 261: 207-214.
  • Fährrolfes, et al., Volkamer, Rarey, (2017). ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acid Res, 45(W1): W337-W343
  • Eid, Turk, Volkamer, Rippmann, Fulle, (2017). KinMap: a web-based tool for interactive navigation through human kinome data. BMC Bioinformatics, 18:16.

Employee

Pratik Dhakal

Wissenschaftliche Hilfskraft

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Henry Webel

research assistant

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