Latest updates

New in silico tox paper published

2021.10.25 · By Andrea Volkamer

Our collaborative work with the BfR - combining in vitro with in silico predictions - is now published in the Environment International Journal: “Quantitative high-throughput phenotypic screening for environmental estrogens using the E-Morph Screening Assay in combination with in silico predictions” (DOI: 10.1016/j.envint.2021.106947).

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Interaction analysis of ~400 MPro structures using PLIPify

2021.10.25 · By Andrea Volkamer

Have a look at our PLIPify work (WIP)! PLIPify provides a wrapper around PLIP, which allows to digest multiple structures at once, performs the mapping of the individual profiles to fingerprints and reports protein-ligand interaction frequencies. It has recently been applied to detect the main interaction within a set of roughly 400 MPro complex structures (large crystal-based fragment screen by Diamond Light Source) in the broader scope of the COVID Moonshot initiative.

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SAVE THE DATE 09.09.21 - Digital Science for Drug Discovery

2021.08.10 · By Corey Taylor

Save the date (Thu. 9. September 2021, 4pm - 5:30pm CET) for an upcoming virtual seminar series, Digital Science for Drug Discovery. Focused on the Berlin region, the series aims to facilitate and enmesh relationships between researchers working within both academia and industry. The over-arching theme? Making efficient and creative use of the wealth of available and growing chemical and biological data combined with powerful computational means at our disposal.

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Deep learning in virtual screening, what's new?

2021.04.23 · By Talia B. Kimber

Interested in the new developments of deep learning in virtual screening ? Check out our review Kimber, 2021. We discuss ligand, protein and complex encodings, deep learning models, data sets, and recent studies. If you want to generate different encodings for your figures, have a look at the GitHub repository!

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FU Softwarepraktikum for 2021: structural alignment

2021.01.08 · By Jaime Rodríguez-Guerra

The new edition of the “Structural Alignment and Superposition” internship is now open for registration! In this internship, an open-source structural alignment Python package for biopolymers, i.e. proteins and ligands, that we started implementing in 2020 will be further developed and released. While diverse structural alignment implementations can be found in visualization software such as PyMol, VMD or UCSF Chimera, a standalone package is currently missing in the Python ecosystem. We have started filling that gap with a modern Python package designed under the current best practices for development, testing and deployment.

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Read about KinFragLib in JCIM

2020.11.06 · By Dominique Sydow

Our KinFragLib project is now published in the Journal of Chemical Modeling and Information: “KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination” (DOI: 10.1021/acs.jcim.0c00839). Kinases are one of the most studied drug targets, resulting in an amount of available data too large to be analyzed manually. In the KinFragLib project, a precise cartography of the ATP-binding site guides the fragmentation of cocrystallized kinase ligands by subpockets. The resulting kinase-focused fragment library allows the analysis of the chemical space by subpocket and is a rich source of inspiration for building novel kinase inhibitors.

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KinFragLib is online!

2020.08.24 · By Dominique Sydow

We are happy to present the results of our KinFragLib project. Aiming to explore and extend the chemical space of kinase inhibitors, we propose a novel subpocket-guided fragmentation and recombination strategy. Take a look at our preprint on ChemRxiv to find our more: “KinFragLib: Exploring the kinase inhibitor space using subpocket-focused fragmentation and recombination”. You can find the reported fragment and combinatorial libraries including all analyses notebooks on our GitHub repository.

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We Are Online!

2020.06.18 · By Andrea Volkamer

We have been working on our new website for a few months and we can finally say that we are happy to announce we are going live! Special thanks to Jaime Rodríguez-Guerra for putting this together!

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