Molecular glues (MGs) offer a unique modality for inducing protein–protein interactions (PPIs), yet their rational design is often hindered by the limitations of static structural data. Here, we present a computational pipeline for the design of cooperative MGs for the FKBP12-MAPRE1 system using replica exchange with...
Shu-Yu Chen, Riccardo Solazzo, Marianne Fouché et al.· Journal of the American Chem...· 0 citations
EDS consistently yields more accurate and statistically robust free-energy estimates compared to the conventional EI scheme for the model system calculations, while a clear advantage is observed for AHFE in the NEQ regime, where less dissipative transitions lead to more reliable free-energy estimates.
Shu-Yu Chen, Enrico Ruijsenaars, P. Hünenberger et al.· Journal of Chemical Theory a...· 0 citations
This work lays the foundation for NNPs where solvation is an integral part of the model, enabling the development of multiscale NNPs for simulating large biomolecular systems.
Moritz Thürlemann, Felix Pultar, Igor Gordiy et al.· Scientific Data· 0 citations
Compared to conventional expectations, it is found that simpler models with interpretable features can achieve competitive performance under rigorous validation protocols and should become a requirement for future ML studies for reaction-yield prediction.
Idil Ismail, Gregory A Landrum, Sereina Riniker· Journal of the American Chem...· 0 citations
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