96 citations · 271 across the 20 of their papers we have counts for
20 papers
Smooth MinMax: A Differentiable Relaxation for Codon Harmonization
Yoonho Jeong, Hyunwoo Choi, Ryan Fernandez Medina Hariri +3
Codon harmonization aims to adapt the coding sequences for heterologous expression while preserving the native-like patterns of frequent and rare codons that may influence local tr…
MOSAIC: Codon Harmonization of Monte Carlo-Based Simulated Annealing for Linked Codons in Heterologous Protein Expression
Yoonho Jeong, Chengcheng Yang, Ryan Fernandez Medina Hariri +6
Codon usage bias has a crucial impact on the translation efficiency and co-translational folding of proteins, necessitating the algorithmic development of codon optimization/harmon…
Understanding Dynamics in Coarse-Grained Models: III. Roles of Rotational Motion and Translation-Rotation Coupling in Coarse-Grained Dynamics
Jaehyeok Jin, Eok Kyun Lee, Gregory A. Voth
This paper series aims to establish a complete correspondence between fine-grained (FG) and coarse-grained (CG) dynamics by way of excess entropy scaling (introduced in Paper I). W…
MolNet: A Chemically Intuitive Graph Neural Network for Prediction of Molecular Properties
Yeji Kim, Yoonho Jeong, Jihoo Kim +3
The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update ato…
InteractionNet: Modeling and Explaining of Noncovalent Protein-Ligand Interactions with Noncovalent Graph Neural Network and Layer-Wise Relevance Propagation
Hyeoncheol Cho, Eok Kyun Lee, Insung S. Choi
Expanding the scope of graph-based, deep-learning models to noncovalent protein-ligand interactions has earned increasing attention in structure-based drug design. Modeling the pro…
Density-Dependent Finite System-Size Effects in Equilibrium Molecular Dynamics Estimation of Shear Viscosity: Hydrodynamic and Configurational Study
Kang-Sahn Kim, Changho Kim, George Em Karniadakis +2
We study the intrinsic nature of the finite system-size effect in estimating shear viscosity of dilute and dense fluids within the framework of the Green-Kubo approach. From extens…