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What docking tool can be easily integrated with the CDK?

Asked by [ Admin ]

I am looking for a script and/or code that calls a docking tool starting from a CDK data model. The parts I am most interested in, is how to set up the input for that docking tool automatically (using that script and/or code), such as initial position of the ligand. Surely this will be a non-trivial piece of code, and any tips towards a full solution would also be much appreciated. Obviously, I have a preference for an Open Source docking tool, but could live with a free docking tool too.

Imported from: http://blueobelisk.stackexchange.com/questions/93

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3 answers

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rajarshi guha [ Editor ]

While a non-trivial piece of code, it's more tedious than difficult. For example, the autodock tools will let you set up a docking run. On the other hand fred_receptor from OE is a very simple to use. Are you thinking of a GUI for docking setup? API calls?

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chem-bla-ics
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API calls… I want to be able to automate as much as possible… if needed, do some orientation in Jmol, but no separate GUis.

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chaninmt [ Editor ]

I have found another software called Biskit (http://biskit.pasteur.fr), which is a structural bioinformatics programs written in Python. It is based on established softwares such as Xplor, Amber, Hex, Prosa, Fold-X, T-Coffee, Hmmer and Modeller. Unfortunately, it appears that the software only supports protein-protein docking.

Tutorials on using Biskit for constructing a workflow for docking is available at:
http://biskit.pasteur.fr/use/workflows/docking
http://biskit.pasteur.fr/use/workflows/flexible-docking

You can read the full article on Biskit at:
http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/6/769

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