Y. Sugita

The paper introduces GENESIS CGDYN, a large-scale coarse-grained MD simulation tool with dynamic load balancing for heterogeneous biomolecular systems, demonstrating its application to IDP droplet fusions and large droplet formation.

This study uses molecular simulations to show that Nanog forms micelle-like clusters in condensates via hydrophobic interactions, with surface domains mediating condensate bridging and DNA recruitment.

This study uses molecular dynamics simulations to investigate how Hero11 proteins regulate TDP-43 condensation through repulsive and attractive interactions, proposing three mechanisms for preventing pathological aggregation.

This study uses molecular dynamics simulations to show that inhibitor size and flexibility affect binding pathways and energetics to c-Src kinase, influencing residence time.

This paper introduces a hidden Markov model to estimate molecular orientations from HS-AFM time-series data, showing improved robustness compared to frame-by-frame analysis.

The paper implements residue-level coarse-grained models in GENESIS to enable large-scale molecular dynamics simulations of biomolecules, improving computational efficiency and handling heterogeneous systems.

This study investigates the structural impact of the D614G mutation in SARS-CoV-2 Spike protein using molecular dynamics simulations, revealing its role in enhancing infectivity and stabilizing the protein structure.

The paper identifies GEM, a nano-liquid hub that integrates growth and immune-evasion signaling to enhance cell survival in mice.

This study identifies multiple conformational states of the SARS-CoV-2 Spike protein's receptor binding domain through molecular dynamics simulations, highlighting structural flexibility important for drug and vaccine design.

This study determines the structure of the Marburg virus NP-RNA complex using cryo-EM, revealing conserved residues critical for nucleocapsid formation and RNA synthesis between MARV and EBOV.

This study determines the molecular mechanisms of two Diels-Alderases that produce enantiomeric decalin scaffolds through structural and computational analyses.

This study shows that GPI-anchoring is essential for the correct transport and glycosylation of an AGP precursor in tobacco cells.

The paper introduces an implicit micelle model (IMIC) for MD simulations of membrane proteins, showing it provides accurate structure predictions with lower computational cost than explicit models.

This study uses molecular dynamics simulations to uncover new conformations and the role of LSGG[Q/E] motifs in ATPase activity regulation in an ABC transporter.

This study investigates the structure of APP-C99 in model membranes, revealing how extra-membrane domains influence Aβ oligomerization and γ-secretase processing.