Results 21 to 30 of about 1,015,340 (312)

Heterogeneity in homogeneous nucleation from billion-atom molecular dynamics simulation of solidification of pure metal

Nature Communications, 2017
Can completely homogeneous nucleation occur? Large scale molecular dynamics simulations performed on a graphics-processing-unit rich supercomputer can shed light on this long-standing issue.
Y. Shibuta, S. Sakane, Eisuke Miyoshi, Shinpei Okita, T. Takaki, M. Ohno   +5 more
semanticscholar   +1 more source

Integration of Molecular Docking Analysis and Molecular Dynamics Simulations for Studying Food Proteins and Bioactive Peptides.

Journal of Agricultural and Food Chemistry, 2022
In silico tools, such as molecular docking, are widely applied to study interactions and binding affinity of biological activity of proteins and peptides.
A. Vidal-Limon, J. E. Aguilar-Toalá, A. Liceaga   +2 more
semanticscholar   +1 more source

Molecular dynamics simulation of uranium nitride oxidation [PDF]

Journal of the Serbian Chemical Society
A molecular dynamic simulation of the uranium mononitride (UN) oxidation in an Ar–O medium in the temperature range of 373–2073 K is performed. The study is performed for UN particles with a crystalline and amorphous structure at an oxygen concentration ...
Galashev Alexander Y., Zaikov Yurii P., Abramova Kseniya A., Rakhmanova Oksana R., Mochalov Yurii S.   +4 more
doaj   +1 more source

Design of New Quinazoline Derivative as EGFR (Epidermal Growth Factor Receptor) Inhibitor through Molecular Docking and Dynamics Simulation

Indonesian Journal of Chemistry, 2020
Erlotinib, Afatinib, and WZ4002 are quinazoline derivative compounds and classified as first, second, and third-generation EGFR inhibitor. All inhibitors have been given directly to cancer patients for many years but find some resistance.
Herlina Rasyid, Bambang Purwono, Harno Dwi Pranowo   +2 more
doaj   +1 more source

Wordom update 2: A user-friendly program for the analysis of molecular structures and conformational ensembles

Computational and Structural Biotechnology Journal, 2023
We present the second update of Wordom, a user-friendly and efficient program for manipulation and analysis of conformational ensembles from molecular simulations.
Angelo Felline, Simone Conti, Michele Seeber, Marco Cecchini, Francesca Fanelli   +4 more
doaj   +1 more source

Disordered but rhythmic—the role of intrinsic protein disorder in eukaryotic circadian timing

FEBS Letters, EarlyView.
Unstructured domains known as intrinsically disordered regions (IDRs) are present in nearly every part of the eukaryotic core circadian oscillator. IDRs enable many diverse inter‐ and intramolecular interactions that support clock function. IDR conformations are highly tunable by post‐translational modifications and environmental conditions, which ...
Emery T. Usher, Jacqueline F. Pelham
wiley   +1 more source

Applications of Molecular Dynamics Simulation in Protein Study

Membranes, 2022
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study ...
Siddharth Sinha, Benjamin Tam, San Ming Wang   +2 more
doaj   +1 more source

The role of histone modifications in transcription regulation upon DNA damage

FEBS Letters, EarlyView.
This review discusses the critical role of histone modifications in regulating gene expression during the DNA damage response (DDR). By modulating chromatin structure and recruiting repair factors, these post‐translational modifications fine‐tune transcriptional programmes to maintain genomic stability.
Angelina Job Kolady, Siyao Wang
wiley   +1 more source

Molecular Dynamics Simulation of Polyacrylamide Adsorption on Calcite

Molecules, 2023
In poorly consolidated carbonate rock reservoirs, solids production risk, which can lead to increased environmental waste, can be mitigated by injecting formation-strengthening chemicals. Classical atomistic molecular dynamics (MD) simulation is employed
Keat Yung Hue, Jin Hau Lew, Maung Maung Myo Thant, Omar K. Matar, Paul F. Luckham, Erich A. Müller   +5 more
doaj   +1 more source

Substrate specificity of Burkholderia pseudomallei multidrug transporters is influenced by the hydrophilic patch in the substrate‐binding pocket

FEBS Letters, EarlyView.
Multidrug transporters BpeB and BpeF from the Gram‐negative pathogen Burkholderia pseudomallei have a hydrophilic patch in their substrate‐binding pocket. Drug susceptibility tests and growth curve analyses using an Escherichia coli recombinant expression system revealed that the hydrophilic patches of BpeB and BpeF are involved in the substrate ...
Ui Okada, Satoshi Murakami
wiley   +1 more source