Free energy perturbation (FEP) methods provide a robust computational framework for predicting protein-ligand binding affinities and have seen increased adoption in drug discovery workflows. Among these, absolute binding free energy (ABFE) calculations are especially valuable as they enable affinity prediction for no...
N. M. Anand, Antonia Panescu, Ronald M. A. Knegtel et al.· Journal of Chemical Theory a...· 0 citations
Biased signaling in G protein-coupled receptors offers therapeutic promise, yet rational design of biased ligands remains challenging due to limited mechanistic understanding. Here, we report a molecular basis for controlling signaling bias at the immunometabolic receptor GPR84. We identify three structurally-match...
Pin-Qi Wang, Xuan Zhang, Abdul-Akim Guseinov et al.· Nature Communications· 0 citations
Ion channels possess selectivity filters that are hardwired to ensure the selective passage of ions. Lysosomal two-pore channels are unusual as they are able to switch their cation selectivity in an agonist-specific manner, allowing differential control of organellar activity. TPC2 is permeable to Ca2+ when activated b...
MDArena is introduced, a benchmark of 50 containerized tasks drawn from active biomolecular simulation projects, spanning 29 molecular systems and 14 broad research protocols, including trajectory analysis, complex system preparation, free-energy protocols, and enhanced sampling, indicating that agents frequently make...
N. M. Anand, W. Hsu, K. Vaccaro et al.· 1 citation
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