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Utilizing protein structure graph embeddings to predict the pathogenicity of missense variants2025 NAR Genomics and Bioinformatics article Biochemistry, Genetics and Molecular Biology Genomics and Rare Diseases Open access
Martin Danner, Matthias Begemann, Miriam Elbracht, Ingo Kurth, Jeremias Krause
2citations -
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access cited by 2 patents
Amelia Villegas-Morcillo, Stavros Makrodimitris, Roeland C. H. J. van Ham, Angel Manuel Gomez, Marcel J. T. Reinders
137citations -
3DDPDs: describing protein dynamics for proteochemometric bioactivity prediction. A case for (mutant) G protein-coupled receptors2023 Journal of Cheminformatics article Computer Science Computational Drug Discovery Methods Open access
Marina Gorostiola González, Remco L. van den Broek, Magdalini Chatzopoulou, Willem Jespers, Adriaan P. IJzerman, Laura H. Heitman, +1 more
6citations -
Evolutionary Engineering of a Cp*Rh(III) Complex-Linked Artificial Metalloenzyme with a Chimeric β-Barrel Protein Scaffold2023 Journal of the American Chemical Society article Chemistry Cyclopropane Reaction Mechanisms Open access
Shunsuke Kato, Akira Onoda, Ulrich Schwaneberg, Takashi Hayashi
28citations -
Highly Repeatable Tissue Proteomics for Kidney Transplant Pathology: Technical and Biological Validation of Protein Analysis Using Liquid Chromatography-Tandem Mass Spectrometry/Mass Spectrometry (LC-MS/MS)2026 Laboratory Investigation article Chemistry Advanced Proteomics Techniques and Applications Open access
Rianne Hofstraat, Kristina Marx, Renata Blatnik, Nike Claessen, Hessel Peters Sengers, Sandrine Florquin, +2 more
0citations -
Genolator enables protein function interpretation using a multimodal large language model fusing genomic and structural interpretation with natural language interaction2026 Genome biology article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Martin Danner, Tanhim Islam, Matthias Begemann, Florian Kraft, Miriam Elbracht, Ingo Kurth, +1 more
0citations -
Unraveling the Phase Behavior, Mechanical Stability, and Protein Reconstitution Properties of Polymer–Lipid Hybrid Vesicles2023 Biomacromolecules article Biochemistry, Genetics and Molecular Biology Lipid Membrane Structure and Behavior Open access
Wagner Augusto Müller, Paul A. Beales, André Rodrigues Muniz, Lars J. C. Jeuken
9citations -
Multimap Targeted Free Energy Estimation: A Mechanical Embedding QM/MM Scheme For Protein-Ligand Affinities2026 Zenodo (CERN European Organization for Nuclear Research) article Computer Science Computational Drug Discovery Methods Open access
Jacques Gay, Andrea Rizzi, Shina Caroline Lynn Kamerlin, Davide Mandelli, Paolo Carloni
0citations -
Photo-controlled delivery of very long chain fatty acids to cell membranes and modulation of membrane protein function2020 Biochimica et Biophysica Acta (BBA) - Biomembranes article Biochemistry, Genetics and Molecular Biology Lipid Membrane Structure and Behavior Open access
Li Kong, Edgar Dawkins, Frederick Campbell, Edith Winkler, Rico J. E. Derks, Martin A. Giera, +3 more
17citations -
AlphaFold Meets De Novo Drug Design: Leveraging Structural Protein Information in Multitarget Molecular Generative Models2024 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Andrius Bernatavicius, Martin Šícho, Antonius P. A. Janssen, Alan Kai Hassen, Mike Preuß, Gerard J. P. van Westen
20citations -
Grubbs-Hoveyda catalysts conjugated to a β-barrel protein: Effect of halide substitution on aqueous olefin metathesis activity2024 Journal of Inorganic Biochemistry article Chemistry Synthetic Organic Chemistry Methods Open access
Aaron A. Ingram, Dong Hua Wang, Ulrich Schwaneberg, Jun Okuda
10citations -
Toward Assay-Aware Bioactivity Model(er)s: Getting a Grip on Biological Context2025 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
Linde Schoenmaker, Enzo G. Sastrokarijo, Laura H. Heitman, Joost B. Beltman, Willem Jespers, Gerard J. P. van Westen
21citations -
The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations2021 Molecules article Biochemistry, Genetics and Molecular Biology Lipid Membrane Structure and Behavior Open access
Hien T. T. Lai, Alejandro Giorgetti, Giulia Rossetti, Toan T. Nguyen, Paolo Carloni, Agata Kranjc
10citations -
Memprot.GPCR-ModSim: modelling and simulation of membrane proteins in a nutshell2024 Bioinformatics article Biochemistry, Genetics and Molecular Biology Receptor Mechanisms and Signaling Open access
Remco L. van den Broek, Xabier Bello, Rebecca V Küpper, Gerard J. P. van Westen, Willem Jespers, Hugo Gutiérrez‐de‐Terán
5citations -
Flexibility of the TRMT10C N-Terminal Domain Helix Explored by Molecular Dynamics Simulations2026 The Journal of Physical Chemistry B article Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics Open access
Gia Linh Hoang, Giulia Rossetti, Carine Tisné, Paolo Carloni
0citations -
Automated assays accelerate bioprocess development for the production of peroxidases in Komagataella phaffii2026 Biotechnology for the Environment article Biochemistry, Genetics and Molecular Biology Enzyme Production and Characterization Open access
Christian Mathis Wagner, Philipp Dante Zinn, Katharina Schwartz, Anton Glieder, Wolfgang Wiechert, Marco Oldiges
0citations -
RNF26 binds perinuclear vimentin filaments to integrate ER and endolysosomal responses to proteotoxic stress2023 The EMBO Journal article Biochemistry, Genetics and Molecular Biology Endoplasmic Reticulum Stress and Disease Open access
Tom Cremer, Lenard M. Voortman, Erik Bos, Marlieke L.M. Jongsma, Laurens R. ter Haar, Jimmy J.L.L. Akkermans, +9 more
36citations