Published in Biophysical Journal (2025), 2025
All-atomistic molecular dynamics simulations of the Tau(210-240)/BIN1 SH3 complex reveal that additional phosphate charges reduce salt-bridge formation by up to 32% and cause a strong preference in Tau for contact with the distal and n-Src loops instead of the RT-Src loop.
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Published in Archiv der Pharmazie (2025), 2025
An integrated computational approach led to the discovery of Hit-3 (CSC089939231), a new nonsteroidal Takeda G protein-coupled receptor 5 (TGR5) modulator, with molecular dynamics simulations suggesting its activation is supported by a hydrogen bond interaction with Tyr240.
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Published in Journal of Chemical Theory and Computation, 2024
This paper is about an investigation made into the disordered regions of p53 using molecular dynamics and machine learning techniques.
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Published in Journal of Chemical Theory and Computation, 2024
This study uses fully atomistic explicit water molecular dynamics simulations to explore the functional landscape of the intrinsically disordered p53 regulatory domain, revealing a detailed understanding of how varying the number of phosphorylated amino acids impacts its conformational dynamics, flexibility, structural effects, protein interactivity, and energy landscapes.
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Published in Journal of Chemical Information and Modeling, 2024
This study introduces an approach to better understand the conformational ensemble (CoE) of intrinsically disordered proteins (IDPs) by decomposing the ensemble of the model peptide histatin 5 into groups separated by their radius of gyration (Rg​) using a combination of small-angle X-ray scattering (SAXS) and all-atomistic molecular dynamics simulations.
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Published in Journal of Chemical Information and Modeling, 2024
This study streamlines the sampling procedure for predicting NMR chemical shifts (CS) in intrinsically disordered proteins (IDPs) by merging dimensionality reduction (DR) (specifically using solvent-accessible surface area (SASA)) and clustering algorithms (CA) to generate clustered ensembles (CEs) that outperform traditional sequential ensembles.
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Published in Energies, 2024
The long-term unsustainability of petroleum-based products is addressed by investigating the direct molecular dynamics simulation of the pyrolysis of methyl linoleate (a biodiesel substitute) to understand the atomistic details of its decomposition and identify alternative, renewable pathways to produce valuable petrochemical precursors like ethene and propene.
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Published in Physical Chemistry and Chemical Physics, 2022
This paper is about the generation of NMR chemical shifts ab-inito from IDP trajectories using a multiscale approach.
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Published in Concepts in Magnetic Resonance, 2019
This paper discusses a method for creating 3D printed models of NMR data using Mathematica and a 3D printer, which can serve as a helpful teaching tool for students to understand complex information in NMR spectra.
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