33 citations · 39 across the 7 of their papers we have counts for
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q-bio.BM2025★ 4 cited
Software package for simulations using the coarse-grained CALVADOS model
Sören von Bülow, Ikki Yasuda, Fan Cao +6
We present the CALVADOS package for performing simulations of biomolecules using OpenMM and the coarse-grained CALVADOS model. The package makes it easy to run simulations using th…
q-bio.BM2021★ 33 cited
Ligand-induced protein dynamics differences correlate with protein-ligand binding affinities: An unsupervised deep learning approach
Ikki Yasuda, Katsuhiro Endo, Eiji Yamamoto +2
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). T…