Zobrazeno 1 - 10
of 15
pro vyhledávání: '"Ryan McGreevy"'
Publikováno v:
eLife, Vol 5 (2016)
Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods,
Externí odkaz:
https://doaj.org/article/a634c22656b84df4bcb1ce5b496cfa36
Autor:
John Ryan McGreevy, Elisson Adrien
Publikováno v:
SSRN Electronic Journal.
Autor:
Ryan McGreevy, Julio D.C. Maia, David J. Hardy, Giacomo Fiorin, Zaida Luthey-Schulten, Aleksei Aksimentiev, Emad Tajkhorshid, James C. Phillips, John E. Stone, Yi Wang, Benoît Roux, João V. Ribeiro, Wei Jiang, Christophe Chipot, Robert D. Skeel, Ronak Buch, Jérôme Hénin, Abhishek Singharoy, Rafael C. Bernardi, Brian K. Radak, Marcelo C. R. Melo, Klaus Schulten, Laxmikant V. Kale
Publikováno v:
Journal of Chemical Physics
Journal of Chemical Physics, American Institute of Physics, 2020, 153 (4), pp.044130. ⟨10.1063/5.0014475⟩
J Chem Phys
Journal of Chemical Physics, American Institute of Physics, 2020, 153 (4), pp.044130. ⟨10.1063/5.0014475⟩
J Chem Phys
International audience; NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on central processing unit (CPU)-and graphics processing unit (GPU)-based architectures. NAMD offers scalable perf
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::b9ba6402af2a0f87d67e384c19fd767f
https://hal.archives-ouvertes.fr/hal-03007668
https://hal.archives-ouvertes.fr/hal-03007668
Publikováno v:
The Journal of Physical Chemistry B. 121:3718-3723
X-ray crystallography and cryo-electron microscopy are two popular methods for the structure determination of biological molecules. Atomic structures are derived through the fitting and refinement of an initial model into electron density maps constr
Autor:
Rafael C. Bernardi, Boon Chong Goh, Ryan McGreevy, Abhishek Singharoy, C. Keith Cassidy, Jodi A. Hadden, Till Rudack, Klaus Schulten
Publikováno v:
Annual Review of Biophysics. 45:253-278
The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving st
Autor:
Jane S. Richardson, Yuhang Wang, Mrinal Shekhar, Emad Tajkhorshid, Abhishek Singharoy, Darren Thifault, Ryan McGreevy, Christopher J. Williams
Publikováno v:
Journal of structural biology. 204(2)
Accurate structure determination from electron density maps at 3–5 A resolution necessitates a balance between extensive global and local sampling of atomistic models, yet with the stereochemical correctness of backbone and sidechain geometries. Mo
Autor:
Ryan McGreevy, Klaus Schulten, Dong Xu, Qufei Li, Eduardo Perozo, Jingfen Zhang, Abhishek Singharoy
Publikováno v:
Acta Crystallographica Section D: Biological Crystallography
A new real-space refinement method for low-resolution X-ray crystallography is presented. The method is based on the molecular dynamics flexible fitting protocol targeted at addressing large-scale deformations of the search model to achieve refinemen
Autor:
Qufei Li, Eduardo Perozo, Klaus Schulten, David Medovoy, Sherry Wanderling, Raymond E. Hulse, Anthony A. Kossiakoff, Carlos A. Villalba-Galea, Abhishek Singharoy, Ryan McGreevy, Benoît Roux, Marcin Paduch
Publikováno v:
Nature Structural & Molecular Biology. 21:244-252
The transduction of transmembrane electric fields into protein motion plays an essential role in the generation and propagation of cellular signals. Voltage-sensing domains (VSD) carry out these functions through reorientations of S4 helix with discr
Publikováno v:
Faraday Discuss.. 169:265-283
Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obta
Publikováno v:
eLife
eLife, Vol 5 (2016)
eLife, Vol 5 (2016)
Two structure determination methods, based on the molecular dynamics flexible fitting (MDFF) paradigm, are presented that resolve sub-5 Å cryo-electron microscopy (EM) maps with either single structures or ensembles of such structures. The methods,