Simple, yet efficient conformational sampling methods for reproducing/predicting biologically rare events of proteins
R Harada - Bulletin of the Chemical Society of Japan, 2018 - academic.oup.com
The biological functions of proteins are strongly related to their conformational transitions. To
elucidate the essential dynamics, molecular dynamics (MD) simulation has become a …
elucidate the essential dynamics, molecular dynamics (MD) simulation has become a …
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 …
PaCS-Toolkit: Optimized Software Utilities for Parallel Cascade Selection Molecular Dynamics (PaCS-MD) Simulations and Subsequent Analyses
S Ikizawa, T Hori, TN Wijaya, H Kono… - The Journal of …, 2024 - ACS Publications
Parallel cascade selection molecular dynamics (PaCS-MD) is an enhanced conformational
sampling method conducted as a “repetition of time leaps in parallel worlds”, comprising …
sampling method conducted as a “repetition of time leaps in parallel worlds”, comprising …
Protein–ligand dissociation simulated by parallel cascade selection molecular dynamics
We investigated the dissociation process of tri-N-acetyl-d-glucosamine from hen egg white
lysozyme using parallel cascade selection molecular dynamics (PaCS-MD), which …
lysozyme using parallel cascade selection molecular dynamics (PaCS-MD), which …
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 …
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 …
Preferential Door for Ligand Binding and Unbinding Pathways in Inhibited Human Acetylcholinesterase
N Kongkaew, K Hengphasatporn… - The Journal of …, 2024 - ACS Publications
Rising global population and increased food demands have resulted in the increased use of
organophosphate pesticides (OPs), leading to toxin accumulation and transmission to …
organophosphate pesticides (OPs), leading to toxin accumulation and transmission to …
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 …
Hybrid Cascade-type molecular dynamics with a Markov state model for efficient free energy calculations
A protocol for calculating free energy landscapes (FELs) is proposed based on a
combination of two cascade-type molecular dynamics (MD) methods, parallel cascade …
combination of two cascade-type molecular dynamics (MD) methods, parallel cascade …