Results 11 to 20 of about 1,994,057 (402)

Molecular dynamics simulation of an entire cell

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. In this perspective, we show how an integrative approach can be employed to model an entire cell, the ...
Stevens, Jan A., Grünewald, Fabian, van Tilburg, P. A. Marco, König, Melanie, Gilbert, Benjamin R., Brier, Troy A., Thornburg, Zane R., Luthey-Schulten, Zaida, Marrink, Siewert J.   +8 more
doaj   +6 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

Molecular Dynamics Simulation for All [PDF]

Neuron, 2018
The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery has expanded dramatically in recent years. These simulations capture the behavior of proteins and other biomolecules in full atomic detail and at very fine temporal resolution.
Scott A. Hollingsworth, Ron O. Dror
openaire   +4 more sources

Molecular dynamics simulation in virus research [PDF]

Frontiers in Microbiology, 2012
Virus replication in the host proceeds by chains of interactions between viral and host proteins. The interactions are deeply influenced by host immune molecules and anti-viral compounds, as well as by mutations in viral proteins. To understand how these interactions proceed mechanically and how they are influenced by mutations, one needs to know the ...
Hirotaka eOde, Hirotaka eOde, Masaaki eNakashima, Masaaki eNakashima, Shingo eKitamura, Shingo eKitamura, Wataru eSugiura, Wataru eSugiura, Hironori eSato   +8 more
openaire   +5 more sources

Color Molecular-Dynamics for High Density Matter [PDF]

Phys.Rev. C61 (2000) 062201, 1999
We propose a microscopic simulation for quark many-body system based on molecular dynamics. Using color confinement and one-gluon exchange potentials together with the meson exchange potentials between quarks, we construct nucleons and nuclear/quark ...
A. Bonasera, A. Ono, A. Ono, A. Ono, C. J. Horowitz, C. T. Traxler, D. H. Boal, G. Baym, H. Feldmeier, H. Satz, I. M. Barbour, J. Aichelin, J. Aichelin, J. C. Collins, K. Saito, M. M. Boyce, M. Oka, P. A. M. Guichon, P. H. Damgaad, S. G. Matinyan, T. Maruyama, T. Maruyama, Tetsuo Hatsuda, Toshiki Maruyama, U. Vogl, W. Pöschl, Y. Koike, Y. Koike, Y. Koike   +28 more
core   +2 more sources

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

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

Molecular dynamics simulations in photosynthesis [PDF]

Photosynthesis Research, 2020
AbstractPhotosynthesis is regulated by a dynamic interplay between proteins, enzymes, pigments, lipids, and cofactors that takes place on a large spatio-temporal scale. Molecular dynamics (MD) simulations provide a powerful toolkit to investigate dynamical processes in (bio)molecular ensembles from the (sub)picosecond to the (sub)millisecond regime and
Nicoletta Liguori, Roberta Croce, Siewert J. Marrink, Sebastian Thallmair   +3 more
openaire   +5 more sources

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

Molecular dynamics simulations [PDF]

Journal of Physics: Condensed Matter, 2004
38 pages, 11 figures, to appear in J.
Fathollah Varnik, Wolfgang Paul, Walter Kob, Kurt Binder, Jürgen Horbach   +4 more
openaire   +4 more sources