We are thrilled to announce the release of TeachOpenCADD Deep Learning (DL) Edition, an expansion of TeachOpenCADD platform! If you are not familiar with TeachOpenCADD platform, more information is provided on its website or here.
The DL edition offers a comprehensive introduction to various deep learning topics with a focus on its application to drug discovery tasks. It empowers learners to explore and understand various concepts in DL field accomodating beginner users to advanced levels.
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Our Berlin team members had the long-awaited opportunity to visit Saarbrücken. Volkamer lab team finally met face-to-face, moving beyond the realm of virtual meetings and creating bonds that strengthens our collaborations and will enrich our work dynamics.
More is yet to come!
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Have a look on our newest publication presenting a method to generate and validate Virtual Control Groups (VCGs) in systemic toxicity studies. This paper highlights the impact of anesthetics on measured electrolytes in animals and presents how these anesthetic protocols can affect the performance of virtual control groups.
This article was published by Alexander, our PhD student at Bayer Pharmaceuticals as a member of the eTRANSAFE Virtual Control Groups team.
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Great collaborative work with IBM research and ETH Zürich is now published in Digital discovery. The model for molecular property prediction is validated on the large proprietary toxicity dataset from our previous study (Webel, 2020), uses uncertainty to improve reliability, reveals cytotoxic motifs via attention and outperforms existing approaches!
You can check the paper on Born, 2023 and the code of the model is available here.
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Floriane holds a bachelor’s degree in life science and bioinformatics and a master’s degree in bioinformatics and in Silico drug design from the University of Paris. She joined our lab in February 2023 as a PhD candidate to be part of the BMBF-funded MORPHEUS project. She will work on the development of deep learning models to predict the effects of substances and identify characteristic fingerprints based on morphological (cell painting) and molecular input data.
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Take a look at our newest opinion paper Machine learning for small molecule drug discovery in academia and industry.
Great collaboration with academic and industry colleagues discussing advances and challenges in molecular machine learning. Despite common overarching goals, we highlight the differences between academic and industry to improve models for e.g. drug selection and share ideas to improve collaborations.
Thanks to all co-authors for working together on this project with such enthusiasm!
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Paula completed her Bioinformatics bachelor’s and master’s at Saarland University. She is joining Volkamer lab as a PhD candidate as part of the NextAID research group, where the focus is on deep learning for drug discovery. She will be working on combining deep learning with fragment based drug design to generate novel ligand candidates for kinase inhibition.
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Michael obtained his PhD under the supervision of Prof. Dr. Verena Wolf. As part of the NextAID team his work focuses on the development of machine learning models for drug discovery.
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We are happy to announce that the lab moved to Saarland University, where we focus on Data Driven Drug Design! We are embedded in a vibrant environment, located in the Center for Bioinformatics and being part of Saarland Informatics Campus as well as the HIPS.
We are thankful for the time at Charité Berlin and are looking forward to many interesting projects and collaborations in Saarbrücken.
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Struc2Drug The latest iteration of Struc2Drug, will be held on Thu 07. April 2022, 4pm - 5pm CET by the Volkamer Lab. Struc2drug is a bimonthly seminar series promoting the exchange between researchers in the interdisciplinary field of structural biology and drug development in Berlin.
Confirmed speakers for the next series include:
Dr. Mikhail Kudryashev (Kudryashev lab, Max Delbrück Center for Molecular Medicine, Berlin) “Activation of the serotonin receptor ion channel 5-HT3 probed by cryo-EM” Vasilii Mikirtumov (Kudryashev lab, Max Delbrück Center for Molecular Medicine, Berlin) “Structure and activation mechanism of ryanodine receptor isoform 1 in native membrane” No registration is needed, please join the meeting via FU berlin at https://fu-berlin.
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