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Molecular dynamics simulation in tissue engineering. [PDF]

Bioimpacts
Rahmani A, Jafari R, Nadri S.
europepmc   +1 more source

Molecular Docking, Molecular Dynamics Simulation, and Pharmacophore-Based Virtual Screening Unveil Natural Compounds with TIM-3 Inhibitory Activity.

J Pharm Bioallied Sci
Alzain AA, Almogaddam MA, Yousif R, Alqarni MH, Foudah AI, Osman W, Elamin KM, Mohamed HM, Moglad E, Ashour A, Samra RM, Mohamed GA, Ibrahim SRM.   +12 more
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Molecular dynamics simulations

Current Opinion in Structural Biology, 2002
Molecular dynamics simulations have become a standard tool for the investigation of biomolecules. Simulations are performed of ever bigger systems using more realistic boundary conditions and better sampling due to longer sampling times. Recently, realistic simulations of systems as complex as transmembrane channels have become feasible.
Chris Oostenbrink, Tomas Hansson, Wilfred F. van Gunsteren   +2 more
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Molecular dynamics simulation and steered molecular dynamics simulation on irisin dimers

Journal of Molecular Modeling, 2018
Irisin is found closely associated with promoting the browning of beige fat cells in white adipose tissue. The crystal structure reveals that irisin forms a continuous inter-subunit β-sheet dimer. Here, molecular dynamics (MD) simulation and steered molecular dynamics (SMD) simulation were performed to investigate the dissociation process and the ...
Chao Lu, Wang Xiaowen, You-Lin Xue, Youtao Song, Zhang Junwei, Qi Gao   +5 more
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Molecular Dynamics Simulation of Nanoindentation [PDF]

, 2004
Molecular dynamics simulations are used to investigate the nucleation and dynamics of dislocations during nanoindentation of a (111) FCC plane. The core structure around the dislocation is visualized by coloring the atoms with deviating coordination number and its Burgers vector is automatically determined.
Kristel Michielsen, Jtm De Hosson, H. De Raedt, Marc Thilo Figge   +3 more
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Molecular dynamics simulations of xDNA

Biopolymers, 2009
AbstractxDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force‐field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5′ G xT A xC xG C xA xG T3′) · (xA5′ C T xG C G xT A xC A3′)
Renjith Thomas, Chellappanpillai Sudarsanakumar, N. V. Unnikrishnan, Mathew K. Varghese   +3 more
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Molecular dynamics simulations of metalloproteins

Current Opinion in Chemical Biology, 2003
Molecular dynamics simulations are now commonly applied to metalloproteins, despite the challenges introduced by the presence of metal ions. Force field parameters are nowadays available also for these 'exotic' atoms and several biological systems have been successfully studied.
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Molecular Dynamics Simulations

2008
Molecular simulation is a very powerful toolbox in modern molecular modeling, and enables us to follow and understand structure and dynamics with extreme detail--literally on scales where motion of individual atoms can be tracked. This chapter focuses on the two most commonly used methods, namely, energy minimization and molecular dynamics, that ...
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