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Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding2025 The Journal of Physical Chemistry B article Computer Science Computational Drug Discovery Methods Open access
Sukrit Singh, Vytautas Gapsys, Matteo Aldeghi, David Schaller, Aziz M. Rangwala, Jessica B. White, +10 more
15citations -
Identification of HLA-E Binding Mycobacterium tuberculosis–Derived Epitopes through Improved Prediction Models2022 The Journal of Immunology article Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Paula Ruibal, Kees L. M. C. Franken, Krista E. van Meijgaarden, Marjolein van Wolfswinkel, Ian Derksen, Ferenc A. Scheeren, +11 more
21citations -
Concanavalin A staining: a potential biomarker to predict cytarabine sensitivity in acute myeloid leukemia2024 Frontiers in Hematology article Biochemistry, Genetics and Molecular Biology Glycosylation and Glycoproteins Research Open access
Tao Zhang, Glenn Marsman, Diego A. Pereira‐Martins, Manfred Wuhrer, Gerwin A. Huls, Valerie R. Wiersma
1citations -
Navigating the complexities of docking tools with nicotinic receptors and acetylcholine binding proteins in the realm of neonicotinoids2024 Ecotoxicology and Environmental Safety article Computer Science Computational Drug Discovery Methods Open access
Zakaria Bouchouireb, Damien Olivier‐Jimenez, Titouan Jaunet‐Lahary, Steeve Hervé Thany, Jean‐Yves Le Questel
14citations -
Identification of Amino Acid Residues, Distal to the Peptide‐Binding Domain, That Confer Serological Distinctions Within Each HLA‐DQB1*02 , *03 , *05 and *06 Antigen Group2026 HLA article Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Shi‐Yuan Meng, Ujjwala Singh, Naiiry Petrosyan, Fred Quiroz, Xiaoliang Yao, Than Than Han, +12 more
0citations -
PMIpred: a physics-informed web server for quantitative protein–membrane interaction prediction2024 Bioinformatics article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Niek van Hilten, Nino Verwei, Jeroen Methorst, Carsten Nase, Andrius Bernatavicius, Herre Jelger Risselada
41citations -
Accurate prediction of HLA class II antigen presentation across all loci using tailored data acquisition and refined machine learning2023 Science Advances article Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Jonas Birkelund Nilsson, Saghar Kaabinejadian, Hooman Yari, Michel G.D. Kester, Peter van Balen, William H. Hildebrand, +1 more
170citations -
Robust principal component analysis‐based prediction of protein‐protein interaction hot spots2021 Proteins Structure Function and Bioinformatics article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Divya Sitani, Alejandro Giorgetti, Mercedes Alfonso‐Prieto, Paolo Carloni
17citations -
Identification and validation of expressed HLA-binding breast cancer neoepitopes for potential use in individualized cancer therapy2021 Journal for ImmunoTherapy of Cancer article Immunology and Microbiology Immunotherapy and Immune Responses Open access
Hannah Reimann, Andrew Nguyen, Zack Sanborn, Charles Joseph Vaske, Stephen Charles Benz, Kayvan Niazi, +17 more
15citations -
Expediting hit-to-lead progression in drug discovery through reaction prediction and multi-dimensional optimization2025 Nature Communications article Computer Science Computational Drug Discovery Methods Open access
David F. Nippa, Kenneth Atz, Yannick Stenzhorn, Alex T. Müller, Andreas Tosstorff, Jörg Benz, +17 more
10citations -
The TNFα-binding domain of the therapeutic antibody adalimumab elicits CD4 T-cell responses in rheumatoid arthritis patients2025 Frontiers in Immunology article Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Mateusz Makuch, Josine van Beek, Carla Ann Wijbrandts, Marja Aalbers, Philippe Stas, Alexander B. Meijer, +7 more
3citations -
IFABP levels predict visceral malperfusion in the first hours after open thoracoabdominal aortic repair2023 Frontiers in Cardiovascular Medicine article Medicine Abdominal vascular conditions and treatments Open access
Panagiotis Doukas, Cathryn Bassett, Hanif Krabbe, Jelle Frankort, Michael Johan Jacobs, Moustafa Elfeky, +1 more
7citations -
Functional evaluation of TCR-pMHC pairs at scale allows in silico TCR reactivity prediction2026 Immunity article Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Marius Messemaker, Bjørn P. Y. Kwee, Živa Moravec, Sam de Paauw, Jos H. M. Urbanus, Daniel Álvarez Salmoral, +17 more
0citations -
Doing More with Less: Accurate and Scalable Ligand Free Energy Calculations by Focusing on the Binding Site2026 Journal of Chemical Information and Modeling article Computer Science Computational Drug Discovery Methods Open access
David Alencar Araripe, Alejandro Díaz‐Holguín, Antti Poso, Gerard J. P. van Westen, Johan Åqvist, Hugo Gutiérrez‐de‐Terán, +1 more
3citations -
Enhanced Sampling Approach to the Induced-Fit Docking Problem in Protein–Ligand Binding: The Case of Mono-ADP-Ribosylation Hydrolase Inhibitors2021 Journal of Chemical Theory and Computation article Computer Science Computational Drug Discovery Methods Open access
Qianqian Zhao, Riccardo Capelli, Paolo Carloni, Bernhard Lüscher, Jinyu Li, Giulia Rossetti
28citations