Name: Extract Training Sets and Batch QSAR

Author: Steven Muskal

Version : 1.0

Created: 8/2007

Modified: N/A

Purpose: These protocols will extract training sets and build Bayesian QSAR models using excerpted data from Eidogen-Sertanty’s Kinase Knowledgebase (KKB). Data are provided for the following Kinase targets: ABL, SRC, and AURKA. Larger data sets can be requested from info@eidogen-sertanty.com.

Requirements: Pipeline Pilot 6.1.1 (collections: Chemistry, Data Modeling)

O/S: PP Server Windows and Linux
PP Client Windows

Limitations: None

Keyword: Kinase QSAR Bayesian Modeling Training Set Extraction

Contents: KKB-Excerpt-ExtractTrainingSets.xml
KKB-Excerpt-Batch-QSAR.xml
Q207-Excerpt_KB_SAR.sdf
Q207-Excerpt_KB_SAR.txt

Installation:

1. Drag the protocols into the Pipeline Pilot client workspace, or drag/drop into one of the Pipeline Pilot client explorer tabs to import it directly in the protocol database.

2. In “Global variables” of KKB-ExtractTrainingSets.xml, update the location of the Excerpt_KB_SAR.* files – i.e. the “inputDir” variable.

3. Run the ExtractTrainingSets protocol then run the Batch-QSAR protocol.

Please Note – Large data sets for three Kinase three targets (ABL, SRC, and AURKA) have been exported from Eidogen-Sertanty’s Kinase Knowledgebase (KKB) - http://www.eidogen-sertanty.com/products_kinasekb.html - provided within the Q207-Excerpt_KB_SAR.* data files. Please reference Eidogen-Sertanty’s KKB database when (re)using these data.