Pack: Natural product likeness filter

Description:

Reference:

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

Libraries

Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer

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

http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf

   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

http://www.ts-concepts.de/cdk-taverna2/plugin/ 

 - 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

Note:

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. 

Description:

 Prerequisite: 

<meta />

CDK -Taverna Plugin 0.5.1

http://www.ts-concepts.de/cdk-taverna2/plugin/

- To run this workflow you need a Score file which is written to text file. 

- This could be generated from ScorerActivity.t2flow

<meta />http://www.myexperiment.org/workflows/2121/download?version=1

Description of input ports :

score_file: Path to file name that has pre computed scores.

Note:

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

file: File name to write out the image of the distribution plot.

Description:

 Prerequisite:  

- CDK -Taverna Plugin 0.5.1

<meta>http://www.ts-concepts.de/cdk-taverna2/plugin/</meta>

- To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed

- This could be generated from GenerateAtomSignatures.t2flow

<meta>http://www.myexperiment.org/workflows/2120/download?version=1</meta>

Description of input ports :

NP_file: needs precomputed Atom_signatures of desired Natural product structural data

SM_file: needs precomputed Atom_signatures of desired Synthetic molecule structural data

Query_file:  needs precomputed Atom_signatures of desired query compound structural data

Note:

While passing file as input for all the above ports it could be passed as list of many files or single file. Since, it loads signatures into memory high heap-space is required.

Score_file: File name to write out the computed natural product likeness scores of query structural data

Fragments_SDF: File name to write out SDF file that has fragments corresponding to scores. Here every atom_signature generated for a molecule is converted into structure and the score generated by the particular fragment is stored as its property. In this way using visualizer we could see the fragments corresponding to score.