Antonia S. J. S. Mey

This study uses molecular dynamics simulations and Markov state models to compare activation mechanisms of tyrosine kinases, revealing kinase-specific conformational ensembles.

GRASP is a graph Transformer that learns molecular structure from ZINC20 data and adapts to ChEMBL bioactivity, achieving better performance than existing models on ADMET prediction tasks.

This paper develops an explainable active learning framework for ligand binding affinity prediction, showing that method choices affect outcomes but dataset characteristics set performance limits.

This paper introduces BALM, a deep learning framework for predicting protein-ligand binding affinity using pre-trained language models, showing better performance than traditional methods in few-shot scenarios.

The paper predicts high-accuracy vibrational spectra from molecular structures using simulations and evaluates methods for IR-based structure determination.

This study compares ABFE and MSM methods for calculating binding free energies of a small molecule to an IDP, finding that MSM provides more consistent results.

This study benchmarks active learning protocols for predicting ligand binding affinity using machine learning models and evaluates the impact of batch size and noise on performance.

The paper evaluates deep learning methods for predicting protein-ligand binding affinity by analyzing the impact of different encodings for proteins and ligands.

The paper shows that mRNAs interact with disordered regions of proteins like MYC to control their activity by enabling specific protein complexes formed in translation sites called TIS granules.

The paper evaluates setup protocols for alchemical free energy calculations on ACK1 inhibitors, finding that manual placement of a bridging water molecule significantly improves accuracy.

This paper introduces a simple geometric model of protein folding that reproduces key ensemble properties of real protein structures, suggesting geometric constraints alone can explain generic features of tertiary structures.

This study uses MD simulations to show that catalytic impairment in CypA mutants is linked to faster nano-microsecond motions of Phe113, challenging the role of millisecond-scale conformational changes in allosteric effects.