Compbio middleware

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.

• 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.

mysql.

openbabel.

wiki

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