Difference between revisions of "Dock"
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| − | [[Category:Software]][[Category:Chemistry | + | [[Category:Software]][[Category:Chemistry]] |
{|<!--Main settings - REQUIRED--> | {|<!--Main settings - REQUIRED--> | ||
|{{#vardefine:app|DOCK}} | |{{#vardefine:app|DOCK}} | ||
|{{#vardefine:url|http://dock.compbio.ucsf.edu}} | |{{#vardefine:url|http://dock.compbio.ucsf.edu}} | ||
|{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | |{{#vardefine:exe|}} <!--Present manual instructions for running the software --> | ||
| − | |{{#vardefine:conf|}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> | + | |{{#vardefine:conf|1}} <!--Enable config wiki page link - {{#vardefine:conf|1}} = ON/conf|}} = OFF--> |
|{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | |{{#vardefine:pbs|}} <!--Enable PBS script wiki page link--> | ||
|{{#vardefine:policy|}} <!--Enable policy section --> | |{{#vardefine:policy|}} <!--Enable policy section --> | ||
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<!--Modules--> | <!--Modules--> | ||
==Required Modules== | ==Required Modules== | ||
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_DOCK_BIN - executable directory | * HPC_DOCK_BIN - executable directory | ||
* HPC_DOCK_DOC - documentation directory | * HPC_DOCK_DOC - documentation directory | ||
| + | * HPC_DOCK_PARAMETERS - directory for parameters | ||
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<!--Additional--> | <!--Additional--> | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | WRITE INSTRUCTIONS ON RUNNING THE ACTUAL BINARY|}} | ||
| + | <!-- | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.|}} | ||
| + | --> | ||
{{#if: {{#var: pbs}}|==PBS Script Examples== | {{#if: {{#var: pbs}}|==PBS Script Examples== | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
Latest revision as of 17:39, 30 June 2024
Description
DOCK addresses the problem of "docking" molecules to each other. In general, "docking" is the identification of the low-energy binding modes of a small molecule, or ligand, within the active site of a macromolecule, or receptor, whose structure is known. A compound that interacts strongly with, or binds, a receptor associated with a disease may inhibit its function and thus act as a drug. Solving the docking problem computationally requires an accurate representation of the molecular energetics as well as an efficient algorithm to search the potential binding modes.
Required Modules
Run module spider DOCK to find out what environment modules are available for this application.
System Variables
- HPC_DOCK_DIR - installation directory
- HPC_DOCK_BIN - executable directory
- HPC_DOCK_DOC - documentation directory
- HPC_DOCK_PARAMETERS - directory for parameters