Difference between revisions of "DOT"
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DOT is a software package for docking macromolecules, including proteins, DNA, and RNA. DOT performs a systematic, rigid-body search of one molecule translated and rotated about a second molecule. The intermolecular energies for all configurations generated by this search are calculated as the sum of electrostatic and van der Waals energies. These energy terms are evaluated as correlation functions, which are computed efficiently with Fast Fourier Transforms. In a typical run, energies for about 108 billion configurations of two molecules can be calculated in a few hours on a few desktop workstations working in parallel. | DOT is a software package for docking macromolecules, including proteins, DNA, and RNA. DOT performs a systematic, rigid-body search of one molecule translated and rotated about a second molecule. The intermolecular energies for all configurations generated by this search are calculated as the sum of electrostatic and van der Waals energies. These energy terms are evaluated as correlation functions, which are computed efficiently with Fast Fourier Transforms. In a typical run, energies for about 108 billion configurations of two molecules can be calculated in a few hours on a few desktop workstations working in parallel. | ||
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| − | == | + | ==Environment 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_{{uc:{{#var:app}}}}_DIR - | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_{{uc:{{#var:app}}}}_BIN - Executable directory | * HPC_{{uc:{{#var:app}}}}_BIN - Executable directory | ||
* HPC_{{uc:{{#var:app}}}}_DOC - Documentation directory | * HPC_{{uc:{{#var:app}}}}_DOC - Documentation directory | ||
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Revision as of 13:29, 13 June 2022
Description
DOT is a software package for docking macromolecules, including proteins, DNA, and RNA. DOT performs a systematic, rigid-body search of one molecule translated and rotated about a second molecule. The intermolecular energies for all configurations generated by this search are calculated as the sum of electrostatic and van der Waals energies. These energy terms are evaluated as correlation functions, which are computed efficiently with Fast Fourier Transforms. In a typical run, energies for about 108 billion configurations of two molecules can be calculated in a few hours on a few desktop workstations working in parallel.
Environment Modules
Run module spider DOT to find out what environment modules are available for this application.
System Variables
- HPC_DOT_DIR - installation directory
- HPC_DOT_BIN - Executable directory
- HPC_DOT_DOC - Documentation directory