Free-energy profiles for membrane permeation of compounds calculated using rare-event sampling methods
The free-energy profile of a compound is an essential measurement in evaluating the
membrane permeation process by means of theoretical methods. Computationally …
membrane permeation process by means of theoretical methods. Computationally …
The role of ATP in solubilizing RNA‐binding protein fused in sarcoma
Intrinsically disordered protein (IDP) plays an important role in liquid–liquid phase
separation (LLPS). RNA‐binding protein fused in sarcoma (FUS) is a well‐studied IDP that …
separation (LLPS). RNA‐binding protein fused in sarcoma (FUS) is a well‐studied IDP that …
Simple, yet powerful methodologies for conformational sampling of proteins
Several biological functions, such as molecular recognition, enzyme catalysis, signal
transduction, allosteric regulation, and protein folding, are strongly related to conformational …
transduction, allosteric regulation, and protein folding, are strongly related to conformational …
Design of electron-donating group substituted 2-PAM analogs as antidotes for organophosphate insecticide poisoning
The use of organophosphate (OPs) pesticides is widespread in agriculture and horticulture,
but these chemicals can be lethal to humans, causing fatalities and deaths each year. The …
but these chemicals can be lethal to humans, causing fatalities and deaths each year. The …
Determination of the Association between Mesotrione Sensitivity and Conformational Change of 4-Hydroxyphenylpyruvate Dioxygenase via Free-Energy Analyses
One widely known herbicide target is 4-hydroxyphenylpyruvate dioxygenase (HPPD). Avena
sativa HPPD is less sensitive to mesotrione (herbicide) than Arabidopsis thaliana HPPD …
sativa HPPD is less sensitive to mesotrione (herbicide) than Arabidopsis thaliana HPPD …
Protein folding pathways extracted by OFLOOD: Outlier FLOODing method
The Outlier FLOODing method (OFLOOD) is proposed as an efficient conformational
sampling method to extract biologically rare events such as protein folding. In OFLOOD …
sampling method to extract biologically rare events such as protein folding. In OFLOOD …
A Structural Refinement Technique for Protein-RNA Complexes Based on a Combination of AI-based Modeling and Flexible Docking: A Study of Musashi-1 Protein
An efficient structural refinement technique for protein-RNA complexes is proposed based
on a combination of AI-based modeling and flexible docking. Specifically, an enhanced …
on a combination of AI-based modeling and flexible docking. Specifically, an enhanced …
Efficient conformational search based on structural dissimilarity sampling: applications for reproducing structural transitions of proteins
Structural Dissimilarity Sampling (SDS) is proposed as an efficient conformational search
method to promote structural transitions essential for the biological functions of proteins. In …
method to promote structural transitions essential for the biological functions of proteins. In …
Structural Validation by the G-Factor Properly Regulates Boost Potentials Imposed in Conformational Sampling of Proteins
Free energy landscapes (FELs) of proteins are indispensable for evaluating thermodynamic
properties. Molecular dynamics (MD) simulation is a computational method for calculating …
properties. Molecular dynamics (MD) simulation is a computational method for calculating …
Ligand binding path sampling based on parallel cascade selection molecular dynamics: LB-PaCS-MD
Parallel cascade selection molecular dynamics (PaCS-MD) is a rare-event sampling method
that generates transition pathways between a reactant and product. To sample the transition …
that generates transition pathways between a reactant and product. To sample the transition …