GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting
نویسندگان
چکیده
منابع مشابه
GPU Accelerated Molecular Dynamics Simulation, Visualization, and Analysis
Please visit www.ks.uiuc.edu/Training/Tutorials/ to get the latest version of this tutorial, to obtain more tutorials like this one, or to join the [email protected] mailing list for additional help.
متن کاملGPU-accelerated visualization of protein dynamics in ribbon mode
Proteins are biomolecules present in living organisms and essential for carrying out vital functions. Inherent to their functioning is folding into different spatial conformations, and to understand these processes, it is crucial to visually explore the structural changes. In recent years, significant advancements in experimental techniques and novel algorithms for post-processing of protein da...
متن کاملxMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures
X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is repo...
متن کاملFlexible fitting of atomic structures into electron microscopy maps using molecular dynamics.
A novel method to flexibly fit atomic structures into electron microscopy (EM) maps using molecular dynamics simulations is presented. The simulations incorporate the EM data as an external potential added to the molecular dynamics force field, allowing all internal features present in the EM map to be used in the fitting process, while the model remains fully flexible and stereochemically corr...
متن کاملDamped-dynamics flexible fitting.
In fitting atomic structures into EM maps, it often happens that the map corresponds to a different conformation of the structure. We have developed a new methodology to handle these situations that preserves the covalent geometry of the structure and allows the modeling of large deformations. The first goal is achieved by working in generalized coordinates (positional and internal coordinates)...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Faraday Discuss.
سال: 2014
ISSN: 1359-6640,1364-5498
DOI: 10.1039/c4fd00005f