Generate Atom Signatures of molecules given SDF as input

Created: 2011-05-13 17:14:06      Last updated: 2011-05-13 19:47:24


Natural Product-likeness Score and Its Application for Prioritization of Compound


Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer

Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland

   The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re-implemented using open source and open data to validate natural product likeness of theoretical metabolite structures while predicting metabolomes.

   These workflows also finds its application in insilico drug designing studies to pre screen candidates for natural product likeness - the original application proposed by Dr. Peter Ertl.


Generate Atom Signatures :

- CDK -Taverna Plugin 0.5.1 

 - This workflow generates atom signatures for individual compounds given the Structural Data File as input. 

  - The atom signatures for natural products, synthetic molecules and other structural data are calculated individually using this workflow


Description of input ports :

Input_SDF : The input SDF file containing compounds of interest


While passing file as input for the above port it could be passed as list of many files or single file. 

Iterations : Number of molecules to be pumped in for each iteration by the SDF file reader

signatures_file : file name with full path for saving the atom signatures

Tagged_SDFile : file name with full path to save the SDF file tagged with Universal Unique IDentifier (UUID). Molecules while progressing through curation steps may break down into fragments. Tagging is done to keep track of molecules while they go through curation steps and could be used to assemble them back during scoring process.

Curated_SDF: file name with full path to store the structures that emerge out as curated ones. This SDF could be later used to view the curated structures by generating their JPEGS using CDK-Taverna/Renderer components or other visualizer like Bioclipse. 



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