Structure Of Biomolecules Through Molecular Dynamics Simulations
نویسندگان
چکیده
منابع مشابه
Coarse-grained molecular dynamics simulations of biomolecules
Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances...
متن کاملMolecular dynamics simulations of biomolecules: long-range electrostatic effects.
Current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number (tens to hundreds of thousands) of atoms are involved over timescales of many nanoseconds. The methodology for treating short-range bonded and van der Waals interactions has matured. However, long-range electrostatic interactions still represent a bottleneck in simulat...
متن کاملIn situ structure and dynamics of DNA origami determined through molecular dynamics simulations.
The DNA origami method permits folding of long single-stranded DNA into complex 3D structures with subnanometer precision. Transmission electron microscopy, atomic force microscopy, and recently cryo-EM tomography have been used to characterize the properties of such DNA origami objects, however their microscopic structures and dynamics have remained unknown. Here, we report the results of all-...
متن کاملSupporting Information: In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
Design of the DNA origami structures. Using caDNAno, we designed the following three DNA origami structures: a straight 6by-3 honeycomb-pleated structure (HC), a straight 4-by-4 squarepleated structure (SQ), and a 6-by-3 honeycomb-pleated structure having a 90◦ programmable bend (HC-90◦). Below, we briefly describe our protocols for obtaining the caDNAno designs. Building a DNA origami structur...
متن کاملDiscrete Molecular Dynamics Simulation of Biomolecules
Biological molecules are highly dynamic and coexist in multiple conformations in solution [1]. Molecular motions are observed on a broad range of time and length scales using spectroscopy and hydrogen–deuterium exchange experiments [2–5]. The internal motions and resulting conformational changes of these molecules play an essential role in their function. Sampling the structural and dynamic pro...
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ژورنال
عنوان ژورنال: Procedia Computer Science
سال: 2019
ISSN: 1877-0509
DOI: 10.1016/j.procs.2019.08.181