THE POTENTIAL OF GRID COMPUTING IN THREE-DIMENSIONAL ELECTRON MICROSCOPY

2004 ◽  
Vol 14 (02) ◽  
pp. 151-162 ◽  
Author(s):  
J. R. Bilbao-Castro ◽  
R. Marabini ◽  
J. M. Carazo ◽  
I. Garcia ◽  
J. J. Fernandez
Keyword(s):  
Electron Microscopy ◽  
Grid Computing ◽  
Three Dimensional ◽  
Computational Grids ◽  
Dimensional Electron ◽  
Wide Range ◽  
High Resolution Structure ◽  
Potential Benefits ◽  
Computationally Intensive ◽  
Resolution Structure

This article describes a potential application of grid computing in structural biology. Three-dimensional electron microscopy allows the investigation of biological structures over a wide range of sizes, from cells to single macromolecules. Knowledge of the structure is critical to understanding the function of biological specimens. However, high resolution structure determination is computationally intensive. This contribution analyzes the potential benefits of grid computing in this field, and draws the conclusion that there are excellent opportunities to take advantage of computational grids.

Grid Computing in 3D Electron Microscopy Reconstruction

2012 ◽  
pp. 881-898
Author(s):  
J.R. Bilbao-Castro ◽  
I. García ◽  
J.J. Fernández
Keyword(s):  
Electron Microscopy ◽  
Grid Computing ◽  
Three Dimensional ◽  
Dimensional Electron ◽  
Reconstruction Process ◽  
Computing Paradigm ◽  
Structural Conformation ◽  
Reconstructed Volume ◽  
Dimensional Reconstruction ◽  
Computational Resources

Three-dimensional electron microscopy allows scientists to study biological specimens and to understand how they behave and interact with each other depending on their structural conformation. Electron microscopy projections of the specimens are taken from different angles and are processed to obtain a virtual three-dimensional reconstruction for further studies. Nevertheless, the whole reconstruction process, which is composed of many different subtasks from the microscope to the reconstructed volume, is not straightforward nor cheap in terms of computational costs. Different computing paradigms have been applied in order to overcome such high costs. While classic parallel computing using mainframes and clusters of workstations is usually enough for average requirements, there are some tasks which would fit better into a different computing paradigm – such as grid computing. Such tasks can be split up into a myriad of subtasks, which can then be run independently using as many computational resources as are available. This chapter explores two of these tasks present in a typical three-dimensional electron microscopy reconstruction process. In addition, important aspects like fault-tolerance are widely covered; given that the distributed nature of a grid infrastructure makes it inherently unstable and difficult to predict.

Grid Computing in 3D Electron Microscopy Reconstruction

2011 ◽  
pp. 392-409
Author(s):  
J.R. Bilbao Castro ◽  
I. Garcia Fernandez ◽  
J. Fernandez
Keyword(s):  
Electron Microscopy ◽  
Grid Computing ◽  
Three Dimensional ◽  
Dimensional Electron ◽  
Reconstruction Process ◽  
Computing Paradigm ◽  
Structural Conformation ◽  
Reconstructed Volume ◽  
Dimensional Reconstruction ◽  
Computational Resources

Three-dimensional electron microscopy allows scientists to study biological specimens and to understand how they behave and interact with each other depending on their structural conformation. Electron microscopy projections of the specimens are taken from different angles and are processed to obtain a virtual three-dimensional reconstruction for further studies. Nevertheless, the whole reconstruction process, which is composed of many different subtasks from the microscope to the reconstructed volume, is not straightforward nor cheap in terms of computational costs. Different computing paradigms have been applied in order to overcome such high costs. While classic parallel computing using mainframes and clusters of workstations is usually enough for average requirements, there are some tasks which would fit better into a different computing paradigm – such as grid computing. Such tasks can be split up into a myriad of subtasks, which can then be run independently using as many computational resources as are available. This chapter explores two of these tasks present in a typical three-dimensional electron microscopy reconstruction process. In addition, important aspects like fault-tolerance are widely covered; given that the distributed nature of a grid infrastructure makes it inherently unstable and difficult to predict.

Three-Dimensional Electron Microscopy of the Clamp Loader Small Subunit from Pyrococcus furiosus

2001 ◽  
Vol 134 (1) ◽  
pp. 35-45 ◽  
Author(s):  
Kouta Mayanagi ◽  
Tomoko Miyata ◽  
Takuji Oyama ◽  
Yoshizumi Ishino ◽  
Kosuke Morikawa
Keyword(s):  
Electron Microscopy ◽  
Pyrococcus Furiosus ◽  
Three Dimensional ◽  
Small Subunit ◽  
Clamp Loader ◽  
Dimensional Electron

scholarly journals Rapid high-resolution structure analysis of small, biotechnologically relevant enzymes by cryo-electron microscopy

2021 ◽  
Author(s):  
Nicole Dimos ◽  
Carl P.O. Helmer ◽  
Andrea M. Chanique ◽  
Markus C. Wahl ◽  
Robert Kourist ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Structural Biology ◽  
Structure Analysis ◽  
Cryo Electron Microscopy ◽  
High Resolution Structure ◽  
Fast Development ◽  
Pharmaceutical Industries ◽  
Exquisite Specificity ◽  
Resolution Structure

Enzyme catalysis has emerged as a key technology for developing efficient, sustainable processes in the chemical, biotechnological and pharmaceutical industries. Plants provide large and diverse pools of biosynthetic enzymes that facilitate complex reactions, such as the formation of intricate terpene carbon skeletons, with exquisite specificity. High-resolution structural analysis of these enzymes is crucial to understand their mechanisms and modulate their properties by targeted engineering. Although cryo-electron microscopy (cryo-EM) has revolutionized structural biology, its applicability to high-resolution structure analysis of comparatively small enzymes is so far largely unexplored. Here, we show that cryo-EM can reveal the structures of ~120 kDa plant borneol dehydrogenases at or below 2 Å resolution, paving the way for the fast development of new biocatalysts that provide access to bioactive terpenes and terpenoids.

26S Proteasome Structure Revealed by Three-dimensional Electron Microscopy

1998 ◽  
Vol 121 (1) ◽  
pp. 19-29 ◽  
Author(s):  
Jochen Walz ◽  
Annette Erdmann ◽  
Mary Kania ◽  
Dieter Typke ◽  
Abraham J Koster ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Three Dimensional ◽  
26S Proteasome ◽  
Dimensional Electron
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