Compbio middleware
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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.
Essential
- Python - 2.7 series
- AMSOL - atomic charge and desolvation penalty calculations required for database building.
- Omega by OpenEye - conformation generation required for database building.
- 3D modeling - PyMol or Chimera
- 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.
Psql. rdkit. Drupal. Chemaxon. mysql. openbabel.