Compbio middleware: Difference between revisions
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We define middleware here to mean whatever comes between your application and the operating system. If you have a better name for it, tell us. | We define middleware here to mean whatever comes between your application and the operating system. If you have a better name for it, tell us. | ||
{{TOCright}} | |||
= Essential = | = Essential = | ||
* [[ | * [[Installing AMSOL]] [[AMSOL]] - atomic charge and desolvation penalty calculations required for database building. | ||
* [[Omega]] by [[OpenEye]] - [[conformation generation]] required for database building. | * [[Omega]] by [[OpenEye]] - [[conformation generation]] required for database building. | ||
* [[Matplotlib]] - currently only needed for analysis plots (enrichment) | * [[Matplotlib]] - currently only needed for analysis plots (enrichment) | ||
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Drupal. | Drupal. | ||
* [[PyMol]] | |||
* [[Chimera]] | |||
* [[Knime]] | |||
* [[Marvin]] and [[InstantJChem]] from [[ChemAxon]] | |||
* [[OpenBabel]] | |||
* [[rdkit]] | |||
* [[psql]] and [[MySQL]] | |||
== Feeware == | |||
* [[pgf]] | |||
* [[CSD]] | |||
* [[Chemaxon]] | |||
* [[OpenEye]] | |||
* [[AMSOL]] | |||
* [[Epik]] and [[ligprep]] from Schrodinger | |||
* [[OpenEye]] | |||
Chemaxon. | Chemaxon. | ||
| Line 32: | Line 52: | ||
wiki | wiki | ||
Return to [[So you want to set up a lab]]. | |||
[[Category:Internal]] | [[Category:Internal]] | ||
[[Category:Sysadmin]] | [[Category:Sysadmin]] | ||
[[Category:Docking]] | [[Category:Docking]] | ||
[[Category:Software]] | |||
Latest revision as of 21:08, 23 May 2024
We define middleware here to mean whatever comes between your application and the operating system. If you have a better name for it, tell us.
Essential
- Installing AMSOL AMSOL - atomic charge and desolvation penalty calculations required for database building.
- Omega by OpenEye - conformation generation required for database building.
- Matplotlib - currently only needed for analysis plots (enrichment)
- MSMS - currently only needed by be_blasti
Recommended
- rdkit - recommended and soon to be essential for the DOCK 3.7 pipeline.
- OGS/GE - queuing system. OpenGridEngine is included in Centos and you do not need to install it separately.
Set up psql/rdkit from scratch
Psql.
rdkit.
Drupal.
Feeware
Chemaxon.
mysql.
openbabel.
wiki
Return to So you want to set up a lab.