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Here is an example of a grid file.
Molecular Docking was initiated by generating a Grid file using Receptor Grid Generation tool of Glide.
One important challenge facing grid computing is the design of a grid file system.
However all data replication schemes lack in providing a grid file system.
The Global Grid Forum defines a Grid File System as a human-readable resource namespace for management of heterogeneous distributed data resources, that can span across multiple autonomous administrative domains.
This paper describes a new Grid File System according to the Global Grid Forum recommendations that integrates heterogeneous data storage resources in grids using standard grid technologies: GridFTP and the Resource Namespace Services, both defined by the Global Grid Forum.
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Grid files containing receptor and binding site information required for molecular docking were prepared using the default options of the Receptor Grid Generation tool with the grid box being centered at the coordinates average of the co-crystallized ligand for each crystallographic structure.
Toyama et al. [34] used grid files to index the camera location and temporal information of videos.
Navarrete et al. [25] utilized R-trees [7] and grid files to index the camera locations of videos.
While the library initially contains type-independent access methods such as B-trees, grid files, and linear hashing, it can also be extended with new methods.
Hence, to improve runtime efficiency and reduce I/O file operations, we modified the AutoDock 4.0 source code to load the energy grid files only once, while docking multiple ligands in a single run.
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