Publications
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2024. A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model. 64:26–41.
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2023. Best Practices of Using AI-Based Models in Crystallography and Their Impact in Structural Biology. J Chem Inf Model.
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2023. Conformational and mechanical stability of the isolated large subunit of membrane-bound [NiFe]-hydrogenase from Cupriavidus necator. Frontiers in Microbiology. 13
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2023. Editorial: In Celebration of Women in Science: Biological Modeling and Simulation. Front Mol Biosci. 10:1175325.
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2023. It Takes Tau to Tango: Investigating the Fuzzy Interaction between the R2-Repeat Domain and Tubulin C-Terminal Tails. Biochemistry. 62:2492–2502.
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2023. Molecular determinants of inhibition of UCP1-mediated respiratory uncoupling.. Nat Commun. 14(1):2594.
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2023. Unwrapping NPT Simulations to Calculate Diffusion Coefficients. Journal of Chemical Theory and Computation. 19:3406–3417.
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2022. Between Two Walls: Modeling the Adsorption Behavior of β-Glucosidase A on Bare and SAM-Functionalized Gold Surfaces.. Langmuir. 38(4):1313-1323.
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2022. Building Biological Relevance Into Integrative Modelling of Macromolecular Assemblies. Frontiers in Molecular Biosciences. 9:826136.
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2022. Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. J. Phys. Chem. B. 126(22):4022-4034.
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2022. Design – a new way to look at old molecules. Journal of Integrative Bioinformatics. 19:20220020.
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2022. Enhanced Sampling Methods for Molecular Dynamics Simulations [Article v1.0]. Living Journal of Computational Molecular Science. 4:1583.
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2022. Human Learning for Molecular Simulations: The Collective Variables Dashboard in VMD.. J Chem Theory Comput. 18(3):1945-1956.
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2022. Modeling the Dynamics of Protein-Protein Interfaces, How and Why? Molecules. 27:1841.
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2022. Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2.. J Chem Inf Model. 62(4):958-970.
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2022. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13
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2022. Symmetry-Adapted Restraints for Binding Free Energy Calculations.. J Chem Theory Comput.
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2022. Tripeptide loop closure: A detailed study of reconstructions based on Ramachandran distributions. Proteins: Structure, Function, and Bioinformatics. 90:858-868.
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2021. Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry. The Journal of Chemical Physics. 154:204101.
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2021. Fast and Accurate Multidimensional Free Energy Integration.. J Chem Theory Comput. 17(11):6789-6798.
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2021. Influences of ssDNA-RecA Filament Length on the Fidelity of Homologous Recombination. Journal of Molecular Biology. 433:167143.
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2021. Mechanistic Insights on Heme-to-Heme Transmembrane Electron Transfer Within NADPH Oxydases From Atomistic Simulations.. Front Chem. 9:650651.
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2021. Modeling Perturbations in Protein Filaments at the Micro and Meso Scale Using NAMD and PTools/Heligeom. Bio-protocol. 11:e4097.
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2021. Moving pictures: Reassessing docking experiments with a dynamic view of protein interfaces.. Proteins.
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2021. When Order Meets Disorder: Modeling and Function of the Protein Interface in Fuzzy Complexes. Biomolecules. 11:1529.