Results 1 to 10 of about 1,164,562 (348)

Molecular dynamics simulation of an entire cell [PDF]

Frontiers in Chemistry, 2023
The ultimate microscope, directed at a cell, would reveal the dynamics of all the cell’s components with atomic resolution. In contrast to their real-world counterparts, computational microscopes are currently on the brink of meeting this challenge.
Jan A. Stevens, Fabian Grünewald, P. A. Marco van Tilburg, Melanie König, Benjamin R. Gilbert, Troy A. Brier, Zane R. Thornburg, Zaida Luthey-Schulten, Siewert J. Marrink   +8 more
doaj   +3 more sources

Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS

BMC Bioinformatics, 2023
Background The molecular dynamics is an approach to obtain kinetic and thermodynamic characteristics of biomolecular structures. The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue
Ivo Henrique Provensi Vieira, Eduardo Buganemi Botelho, Thales Junior de Souza Gomes, Roger Kist, Rafael Andrade Caceres, Fernando Berton Zanchi   +5 more
doaj   +2 more sources

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   +2 more sources

Validation of molecular dynamics simulation [PDF]

Journal of Chemical Physics, 1998
How the results obtained by computer simulation of molecular systems can be validated is considered. The overall quality of the simulated properties of a molecular system will depend on (i) the quality of the theory or model, (ii) the accuracy of the ...
Wilfred F van Gunsteren, Alan E Mark
exaly   +2 more sources

Molecular dynamics simulation in concrete research: A systematic review of techniques, models and future directions [PDF]

Journal of Building Engineering, 2023
This paper presents a comprehensive review of the application of molecular dynamics simulation in concrete research. The study addresses the background and significance of the topic, providing an overview of the principles, applications, and types of ...
Salim Barbhuiya
exaly   +2 more sources

Molecular dynamics simulation study of ultrasound induced cavitation [PDF]

Ultrasonics Sonochemistry
Cavitation, though widely studied, has aspects that remain poorly understood, especially at the microlevel. This study employs molecular dynamics simulations using LAMMPS to investigate cavitation processes under sinusoidal ultrasonic forces, examining ...
Weixiang Lin, Xudong Duan, Song He, Jiarui Wang, Simin Wang   +4 more
doaj   +2 more sources

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials [PDF]

arXiv.org, 2023
Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials.
Peter K. Eastman, Raimondas Galvelis, Raúl P. Peláez, C. Abreu, Stephen E. Farr, Emilio Gallicchio, Anton Gorenko, Mike Henry, Frank Hu, Jing Huang, Andreas Krämer, Julien Michel, Joshua A. Mitchell, Vijay S. Pande, J. P. Rodrigues, Jaime Rodríguez-Guerra, Andrew C. Simmonett, Jason M. Swails, Ivy Zhang, J. Chodera, G. D. Fabritiis, T. Markland   +21 more
semanticscholar   +2 more sources

Modified Protein-Water Interactions in CHARMM36m for Thermodynamics and Kinetics of Proteins in Dilute and Crowded Solutions

Molecules, 2022
Proper balance between protein-protein and protein-water interactions is vital for atomistic molecular dynamics (MD) simulations of globular proteins as well as intrinsically disordered proteins (IDPs).
Daiki Matsubara, Kento Kasahara, Hisham M. Dokainish, Hiraku Oshima, Yuji Sugita   +4 more
doaj   +1 more source

Engineering of Ocriplasmin Variants by Bioinformatics Methods for the Reduction of Proteolytic and Autolytic Activities [PDF]

Iranian Journal of Medical Sciences, 2021
Background: Ocriplasmin has been developed for the induction of posterior vitreous detachment in patients with vitreomacular adhesion. At physiological pH, ocriplasmin is susceptible to autolytic and proteolytic degradation, limiting its activity ...
Roghayyeh Baghban, Safar Farajnia, Younes Ghasemi, Mojtaba Mortazavi, Samaneh Ghasemali, Mostafa Zakariazadeh, Nosratollah Zarghami, Nasser Samadi   +7 more
doaj   +1 more source

Reduced efficacy of a Src kinase inhibitor in crowded protein solution

Nature Communications, 2021
The intracellular compartment is a crowded environment. Here, the authors use molecular dynamics (MD) simulations to assess inhibitor binding to c-Src kinase and show how ligand binding pathways differ in crowded and dilute protein solutions ...
Kento Kasahara, Suyong Re, Grzegorz Nawrocki, Hiraku Oshima, Chiemi Mishima-Tsumagari, Yukako Miyata-Yabuki, Mutsuko Kukimoto-Niino, Isseki Yu, Mikako Shirouzu, Michael Feig, Yuji Sugita   +10 more
doaj   +1 more source