Molecular dynamics
View article: ELMO2 molecular dynamics
ELMO2 molecular dynamics Open
Dataset title: ELMO2 molecular dynamicsDescription: Full MD trajectory used for ensemble docking and RMSD/RMSF analyses in the study.Simulation software: GROMACS 2023.2Force field: CHARMM36Temperature: 303 KSolvent: TIP3P water with 0.15 M…
View article: ELMO2 molecular dynamics
ELMO2 molecular dynamics Open
Dataset title: ELMO2 molecular dynamicsDescription: Full MD trajectory used for ensemble docking and RMSD/RMSF analyses in the study.Simulation software: GROMACS 2023.2Force field: CHARMM36Temperature: 303 KSolvent: TIP3P water with 0.15 M…
View article: Conserved nsp3 TM2–Y Region in Nidoviruses / MD results
Conserved nsp3 TM2–Y Region in Nidoviruses / MD results Open
Positive-strand RNA viruses remodel host intracellular membranes to form replication organelles in cytoplasm. SARS-CoV-2 and other coronaviruses, which belong to Nidovirales order, replicate within double-membrane vesicles (DMVs) derived f…
View article: Mechanistic insights into CFTR function from molecular dynamics analysis of electrostatic interactions
Mechanistic insights into CFTR function from molecular dynamics analysis of electrostatic interactions Open
MD simulations of human CFTR (PDB 6O2P):Equilibrium MD simulations were performed on the ATP-bound CFTR structure, with and without the potentiator VX-770 (Ivacaftor). The protein is embedded in a heterogeneous lipid bilayer composed of PO…
View article: Mechanistic insights into CFTR function from molecular dynamics analysis of electrostatic interactions
Mechanistic insights into CFTR function from molecular dynamics analysis of electrostatic interactions Open
MD simulations of human CFTR (PDB 6O2P)Equilibrium MD simulations were performed on the ATP-bound CFTR structure, with and without the potentiator VX-770 (Ivacaftor). The protein is embedded in a heterogeneous lipid bilaye…
View article: Virtual screening, molecular docking, and molecular dynamics simulation reveal new insights into RNA polymerase inhibition for anti-tuberculosis drug discovery.
Virtual screening, molecular docking, and molecular dynamics simulation reveal new insights into RNA polymerase inhibition for anti-tuberculosis drug discovery. Open
This study highlights the effectiveness of combining virtual screening, molecular docking, MD simulations, and MM-PBSA analysis in identifying promising RNAP inhibitors. The results establish a strong foundation for further experimental va…
View article: CodeEntropy
CodeEntropy Open
CodeEntropy is a Python package for calculating configurational entropy from molecular dynamics simulations using the multiscale cell correlation (MCC) method. It enables multiscale analysis of atomic fluctuations to quantify molecular fle…
View article: CodeEntropy
CodeEntropy Open
CodeEntropy is a Python package for calculating configurational entropy from molecular dynamics simulations using the multiscale cell correlation (MCC) method. It enables multiscale analysis of atomic fluctuations to quantify molecular fle…
View article: Active Learning for Transport Property Prediction in CO <sub>2</sub> –Hydrocarbon Systems: A Multifidelity Approach Integrating Molecular Dynamics and Experiments
Active Learning for Transport Property Prediction in CO <sub>2</sub> –Hydrocarbon Systems: A Multifidelity Approach Integrating Molecular Dynamics and Experiments Open
View article: Effects of training machine-learning potentials for radiation damage simulations using different pseudopotentials
Effects of training machine-learning potentials for radiation damage simulations using different pseudopotentials Open
View article: Exploring organic chemical space for materials discovery using crystal structure prediction-informed evolutionary optimisation
Exploring organic chemical space for materials discovery using crystal structure prediction-informed evolutionary optimisation Open
Organic molecular crystals offer a broad spectrum of potential applications. The vast number of possible molecules is both an opportunity and a challenge, because of the prohibitive expense of exhaustively searching chemical space to find …
View article: Structures and files for MD simulations of ternary complexes FKBP12-FRAP-rapamycin and FKBP12-CEP250-WDB002
Structures and files for MD simulations of ternary complexes FKBP12-FRAP-rapamycin and FKBP12-CEP250-WDB002 Open
The directory contains the structures and files used to start molecular dynamics simulations of apo and holo forms of the ternary complexes FKBP12-FRAP-rapamycin and FKBP12-CEP250-WDB002 as well as the binary complexes: FKBP12-rapamycin, F…
View article: Fast machine learned $α$-Fe-H interatomic potential for hydrogen embrittlement
Fast machine learned $α$-Fe-H interatomic potential for hydrogen embrittlement Open
In this work, we present a machine-learned interatomic potential for the $α$-Fe-H system based on the tabulated Gaussian Approximation Potential (tabGAP) formalism. Trained on a Density Functional Theory (DFT) dataset of atomic configurati…
View article: Replication Data for: Field-Driven Simulations to Probe the Impact of Ionic Correlations on Solution Transport Coefficients in Binary, Ternary, and Reciprocal Quaternary Aqueous Electrolytes
Replication Data for: Field-Driven Simulations to Probe the Impact of Ionic Correlations on Solution Transport Coefficients in Binary, Ternary, and Reciprocal Quaternary Aqueous Electrolytes Open
Ionic correlations play a critical role in governing transport properties of mixed-salt aqueous electrolyte solutions, yet their quantitative characterization remains challenging, particularly for multicomponent aqueous systems. Here, we d…
View article: Structural details of helix-mediated multimerization of the conserved region of TDP-43 C-terminal domain
Structural details of helix-mediated multimerization of the conserved region of TDP-43 C-terminal domain Open
Pathological inclusions of the C-terminal domain (CTD) of TAR DNA binding protein-43 (TDP-43) are neurodegenerative hallmarks in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia, yet CTD’s aggregation propensity complicates …
View article: Trans-scale crystal dynamics for controlling kinetic responses in organic molecular systems
Trans-scale crystal dynamics for controlling kinetic responses in organic molecular systems Open
View article: From Static Pathways to Dynamic Mechanisms: A Committor-Based Data-Driven Approach to Chemical Reactions
From Static Pathways to Dynamic Mechanisms: A Committor-Based Data-Driven Approach to Chemical Reactions Open
As computational chemistry methods evolve, dynamic effects have been increasingly recognized to govern chemical reaction pathways in both organic and inorganic systems. Here, we introduce a committor-based workflow that integrates a path-c…
View article: Data publication: Ab initio density functional theory approach to warm dense hydrogen: from density response to electronic correlations
Data publication: Ab initio density functional theory approach to warm dense hydrogen: from density response to electronic correlations Open
KSDFT simulation results for static structure factors, dynamic response functions, and results of MD simulations.
View article: Mechanistic insights into CFTR function from molecular dynamics analysis of electrostatic interactions
Mechanistic insights into CFTR function from molecular dynamics analysis of electrostatic interactions Open
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is an ATP-gated anion channel whose function is tightly linked to its conformational dynamics and is influenced by the composition of its membrane lipid environment. Despite hi…
View article: Surface structure of water from soft X-ray second harmonic generation
Surface structure of water from soft X-ray second harmonic generation Open
The microscopic structure of water’s surface is crucial to many natural and industrial processes, but studying its hydrogen bond (H-bond) network directly remains challenging due to the required interfacial sensitivity of experimental tech…
View article: Different Rise Times of Atomic Br M$_{4,5}$ 3d$_{3/2,5/2}$ Core Level Absorptions during Br$_{2}$ C $^{1}Π_{u}$ $1_{u}$ State Dissociation via Extreme Ultraviolet Transient Absorption Spectroscopy
Different Rise Times of Atomic Br M$_{4,5}$ 3d$_{3/2,5/2}$ Core Level Absorptions during Br$_{2}$ C $^{1}Π_{u}$ $1_{u}$ State Dissociation via Extreme Ultraviolet Transient Absorption Spectroscopy Open
The reported ''dissociation times'' for the Br$_{2}$ C ($^{1}Π_{u}$ $1_{u}$) state by various measurement methods differ widely across the literature (30 to 340 fs). We consider this issue by investigating attosecond extreme ultraviolet (X…
View article: DNA Dynamic Regulation Theory Based on Potassium Channel “Origami Windmill” Model
DNA Dynamic Regulation Theory Based on Potassium Channel “Origami Windmill” Model Open
This article proposes an original DNA origami windmill model, based on the potassium channel “origami windmill” model, to systematically reveal a new molecular mechanism of DNA dynamic regulation. The core structural feature of this model …
View article: Chiral Recognition Mechanism of 2,13-Bis(hydroxymethyl)-[7]thiaheterohelicene on Ag(111) Investigated by STM and MD Simulation
Chiral Recognition Mechanism of 2,13-Bis(hydroxymethyl)-[7]thiaheterohelicene on Ag(111) Investigated by STM and MD Simulation Open
We investigated the adsorption and aggregation properties of 2,13-bis(hydroxymethyl)-[7]thiaheterohelicene ([7]TH-diol) on the Ag(111) surface by scanning tunneling microscopy (STM) and molecular dynamics (MD) simulation. STM observation r…
View article: Chain ends excite polymer cooperative motion
Chain ends excite polymer cooperative motion Open
Among glasses, polymers stand out as the chain connectivity endows them with distinct properties in glass formation, among them the transition temperature ( T g ) and dynamic fragility ( m ) varying with chain length. Here, we resolve the …
View article: Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1)
Impact of anionic lipids on the energy landscape of conformational transition in anion exchanger 1 (AE1) Open
Anion Exchanger 1 (AE1) is an elevator-type transporter that plays a key role in acid-base homeostasis of erythrocytes. Here, we report three high-resolution cryo-electron microscopy (cryo-EM) structures of distinct states of AE1: two inwa…
View article: Systematic In-silico Analysis of Fisetin-Proteins Interactions Revealing the PTGS2 as a Potential Therapeutic Target
Systematic In-silico Analysis of Fisetin-Proteins Interactions Revealing the PTGS2 as a Potential Therapeutic Target Open
Fisetin is a nutraceutical that provides many health benefits, including anticancer, anti-aging, anti-inflammatory, and antidiabetic activities. The present study revealed the molecular mechanism of fisetin through the PCI and PPI interact…
View article: Formulation Optimization of Sinomenine-Loaded Nanostructured Lipid Carriers Based on Molecular Dynamics Simulations and Evaluation of Pharmacological Efficacy in Rheumatoid Arthritis
Formulation Optimization of Sinomenine-Loaded Nanostructured Lipid Carriers Based on Molecular Dynamics Simulations and Evaluation of Pharmacological Efficacy in Rheumatoid Arthritis Open
Sinomenine (SIN), as a potential therapeutic agent for rheumatoid arthritis (RA), exhibits advantages such as non-addictiveness. However, its low aqueous solubility and poor membrane permeability result in limited bioavailability, which co…
View article: Identification of a novel dual-targeting peptide inhibitor of SARS-CoV-2 RBD and NRP1 through structure-based virtual screening
Identification of a novel dual-targeting peptide inhibitor of SARS-CoV-2 RBD and NRP1 through structure-based virtual screening Open
Background The continuous mutations of SARS-CoV-2 have enhanced its transmissibility and immune escape capabilities. Its invasion into cells relies on the binding of the receptor-binding domain (RBD) of the spike (S) protein to host recept…
View article: ThermoPCD 2.0: an updated database of molecular dynamics trajectories of antibody-antigen complexes relevant for infectious diseases and allergies at physiologic and fever-range temperatures
ThermoPCD 2.0: an updated database of molecular dynamics trajectories of antibody-antigen complexes relevant for infectious diseases and allergies at physiologic and fever-range temperatures Open
View article: Cryo-ET and MD simulations reveal that dynein-2 is tuned for binding to the A-tubule of the ciliary doublet
Cryo-ET and MD simulations reveal that dynein-2 is tuned for binding to the A-tubule of the ciliary doublet Open
Eukaryotic cilia and flagella are thin structures present on the surface of cells, playing vital roles in signaling and cellular motion. Cilia assembly depends on intraflagellar transport (IFT) along doublet microtubules (doublets). Unlike…