Johannes Schimunek
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View article: Machine Learning-Driven Optimization of Specific, Compact, and Efficient Base Editors via Single-Round Diversification
Machine Learning-Driven Optimization of Specific, Compact, and Efficient Base Editors via Single-Round Diversification Open
Cytosine and adenosine base editors show great potential in research and clinical applications. Current iterations of the deaminase—the enzyme used to create precise single-nucleotide changes via base editing—exhibit various off-target eff…
View article: MHNfs: Prompting In-Context Bioactivity Predictions for Low-Data Drug Discovery
MHNfs: Prompting In-Context Bioactivity Predictions for Low-Data Drug Discovery Open
Today's drug discovery increasingly relies on computational and machine learning approaches to identify novel candidates, yet data scarcity remains a significant challenge. To address this limitation, we present MHNfs, an application speci…
View article: Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences Open
Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures. W…
View article: A community effort in SARS‐CoV‐2 drug discovery
A community effort in SARS‐CoV‐2 drug discovery Open
The COVID‐19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small‐molecule drugs that are widely available, including i…
View article: Context-enriched molecule representations improve few-shot drug discovery
Context-enriched molecule representations improve few-shot drug discovery Open
A central task in computational drug discovery is to construct models from known active molecules to find further promising molecules for subsequent screening. However, typically only very few active molecules are known. Therefore, few-sho…
View article: A community effort to discover small molecule SARS-CoV-2 inhibitors
A community effort to discover small molecule SARS-CoV-2 inhibitors Open
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including i…
View article: JEDI Billion Molecules against Covid-19: compounds synthesized
JEDI Billion Molecules against Covid-19: compounds synthesized Open
On May 4th 2020 a GrandChallenge entitled "Billion molecules against Covid-19" was launched by the Joint European Disruptive Initiative (JEDI). Teams from all over the world provided lists of compounds with suspected inhibitory properties …
View article: JEDI Billion Molecules against Covid-19: compounds synthesized
JEDI Billion Molecules against Covid-19: compounds synthesized Open
On May 4th 2020 a GrandChallenge entitled "Billion molecules against Covid-19" was launched by the Joint European Disruptive Initiative (JEDI). Teams from all over the world provided lists of compounds with suspected inhibitory properties …
View article: JEDI Billion Molecules against Covid-19: compounds synthesized
JEDI Billion Molecules against Covid-19: compounds synthesized Open
On May 4th 2020 a GrandChallenge entitled "Billion molecules against Covid-19" was launched by the Joint European Disruptive Initiative (JEDI). Teams from all over the world provided lists of compounds with suspected inhibitory properties …
View article: Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors\n using deep neural networks
Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors\n using deep neural networks Open
Due to the current severe acute respiratory syndrome coronavirus 2\n(SARS-CoV-2) pandemic, there is an urgent need for novel therapies and drugs.\nWe conducted a large-scale virtual screening for small molecules that are\npotential CoV-2 i…