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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 -
LogoMotif: A Comprehensive Database of Transcription Factor Binding Site Profiles in Actinobacteria2024 Journal of Molecular Biology article Biochemistry, Genetics and Molecular Biology Bacterial Genetics and Biotechnology Open access
Hannah E. Augustijn, Dimitris Karapliafis, K. Joosten, Sébastien Rigali, Gilles P. van Wezel, Marnix H. Medema
20citations -
Prediction models for hormone receptor status in female breast cancer do not extend to males: further evidence of sex-based disparity in breast cancer
Subarnarekha Chatterji, Marko van Treeck, Chiara Maria Lavinia Loeffler, Oliver Lester Saldanha, Gregory Patrick Veldhuizen, Didem Çifçi, +4 more
8citations -
Fine tuning of long-range interactions to describe the binding of adamantane and diamantane derivatives to a Cucurbit[7]uril-based synthetic receptor: Insights from metadynamics simulations2025 The Journal of Chemical Physics article Chemistry Supramolecular Chemistry and Complexes Open access
Amal Vijay, Giacomo Salvadori, Frank Biedermann, Giulia Rossetti, Paolo Carloni, Davide Mandelli
0citations -
Cord blood levels of insulin‐like growth factor‐1 and insulin‐like growth factor binding protein‐3 correlate with perinatal brain development in fetal congenital heart disease2025 Ultrasound in Obstetrics and Gynecology article Medicine Congenital Heart Disease Studies Open access
Maaike Nijman, Nathalie H.P. Claessens, Johannes M. P. J. Breur, Lieke Reijn, Nicolaas J. G. Jansen, Inge M van Ooijen, +6 more
2citations -
PTX3 structure determination using a hybrid cryoelectron microscopy and AlphaFold approach offers insights into ligand binding and complement activation2022 Proceedings of the National Academy of Sciences article Immunology and Microbiology Biomarkers in Disease Mechanisms Open access
Dylan P. Noone, Douwe J. Dijkstra, Teun T. van der Klugt, Peter A. van Veelen, Arnoud H. de Ru, Paul J. Hensbergen, +2 more
45citations -
Association Between Low Sex Hormone–Binding Globulin and Increased Risk of Type 2 Diabetes Is Mediated by Increased Visceral and Liver Fat: Results From Observational and Mendelian Randomization Analyses
Theresa A Stangl, Chantal Maria Wiepjes, Roelof A. J. Smit, Astrid van Hylckama Vlieg, Hildo J. Lamb, Jeroen H. P. M. van der Velde, +7 more
17citations -
Mutated DNMT3A creates a public HLADQ- binding neoantigen on acute myeloid leukemia2025 Frontiers in Immunology article Immunology and Microbiology Immunotherapy and Immune Responses Open access
Dyantha I. van der Lee, Eva M. Argiro, Sebastiaan N. J. Laan, M. Willy Honders, Rob C. M. de Jong, Nadine Struckman, +2 more
3citations -
Binding pose depth modulates photoswitchable ligands’ efficacy at the 5-HT2A receptor2026 Communications Chemistry article Biochemistry, Genetics and Molecular Biology Receptor Mechanisms and Signaling Open access
Verena Weber, Giacomo Salvadori, Federico Natale, Hubert Gerwe, Michael W. Decker, Paolo Carloni, +1 more
0citations -
Binding pose depth modulates photoswitchable ligands’ efficacy at the 5-HT2A receptor2026 Communications Chemistry article Biochemistry, Genetics and Molecular Biology Receptor Mechanisms and Signaling Open access
Verena Weber, Giacomo Salvadori, Federico Natale, Hubert Gerwe, Michael W. Decker, Paolo Carloni, +1 more
0citations -
Modeling Peptide–Protein Interactions by a Logo-Based Method: Application in Peptide–HLA Binding Predictions2024 Molecules article Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Irini Atanas Doytchinova, Mariyana Atanasova, Antonio Fernandez, Francisco Javier Moreno, Frits Koning, Ivan Dimitrov
6citations -
bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria2024 Nature Communications article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Guillermo Guerrero-Egido, Adrián Pintado, Kevin M. Bretscher, Luisa M. Arias-Giraldo, Joseph Nathaniel Paulson, Herman P. Spaink, +6 more
29citations -
Evidence of task-triggered retrieval of the previous response: a binding perspective on response-repetition benefits in task switching2023 Psychonomic Bulletin & Review article Neuroscience Neural and Behavioral Psychology Studies Open access
Elena Benini, Malte Möller, Iring Koch, Andrea M. Philipp, Ruyi Qiu, Susanne Mayr
3citations -
Surface Ig variable domain glycosylation affects autoantigen binding and acts as threshold for human autoreactive B cell activation2022 Science Advances article Biochemistry, Genetics and Molecular Biology Glycosylation and Glycoproteins Research Open access
Theresa Kissel, Changrong Ge, Lise Hafkenscheid, Joanneke C. Kwekkeboom, Linda M. Slot, Marco Cavallari, +18 more
77citations -
Molecular Modeling of Protein–Peptide Complexes Mimicking Factor Xa–Prothrombin Using AlphaFold-Multimer and Molecular Dynamics Simulations for Functional Prediction2026 Journal of Chemical Information and Modeling article Medicine Blood Coagulation and Thrombosis Mechanisms
Dejvid Veizaj, David Alonzo Poole III, Ka Lei Cheung, Jos V. Flier, Pieter H. Reitsma, Daniël Verhoef, +2 more
1citations -
Tuning the Binding Strength of Even and Uneven Hydrogen-Bonded Arrays with Remote Substituents2020 The Journal of Physical Chemistry A article Chemistry Crystallography and molecular interactions Open access
Stephanie C. C. van der Lubbe, Anissa Haim, Thor van Heesch, Célia Fonseca Guerra
16citations -
Geometrical benchmarking and analysis of redox potentials of copper(I/ II ) guanidine‐quinoline complexes: Comparison of semi‐empirical tight‐binding and DFT methods and the challenge of describing the entatic state (part III )2022 Journal of Computational Chemistry article Physics and Astronomy Advanced Chemical Physics Studies Open access
Lukas Raßpe-Lange, Alexander Hoffmann, Christoph Gertig, Joshua Heck, Kai O. Leonhard, Sonja Herres‐Pawlis
13citations