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 Application Catalog |
DOG
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Solves the geometric docking problem for planar and spatial sets.
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Category: Life Sciences
Sub Category: Computational Chemistry
Publisher: Michel Petitjean
Date Published: 2002
Version: 1.0
Pricing: License,free
Runtime: $1/CPU-hr.
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A CPU-hr. is the aggregate CPU time spent across all machines, rounded up to the nearest hour (e.g., a task running on 1,000 CPUs for one minute = 1,000 CPU minutes or approximately 17 CPU hours, costing you only $17).
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Key Features
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- Algorithm provides the variance of the population of the squared distances defined by the input pairs, and the optimal translation and rotation.
- Results provide the coordinates of the optimally docked atom-pairs.
- Connectivity and charges are not used. No relevant initial orientation is needed before docking.
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Description |
DOG reads the Cartesian coordinates of two molecules, then translates and rotates the second molecule for docking with the first molecule. The docking is performed via minimization of the shape complementarity coefficient for all translations and rotations of the mixtures. A pairwise correspondence between two equal length ranges of atoms is input. When each of the two molecules is a single nucleotidic strand in PDB/NDB format, the pairwise correspondence is defined from the atom-pairs enabling potential hydrogen bonds.
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Technical Information |
The two input molecules should be combined into a single file prior to execution.
The number of atoms is currently limited to 15000 for each molecule. The source has to be recompiled to read larger molecules.
For the NUCLEO parameter, entering Y activates the automatic detection of potential hydrogen bonds from atom labeling analysis, provided that the format is PDB. Three atom pairs are included in the pairwise correspondence for the CG or GC base pairs, and two atom pairs are included for the AT, TA, AU or UA base pairs. Entering N deactivates the option. |
Publisher Information |
Michel Petitjean
DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bât. 528
91191 Gif-sur-Yvette Cedex, France.
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Pricing and Payment Information |
License: Free
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