Dear Colleagues:
Please find below can evaluate the performance a 3rd party conformer generation algorithm and directly compare the analysis results with another Forum posted protocol entitled "Conformational Modeling Building Methods using X-Ray Bound Ligands" (http://community.accelrys.com/message/1193).
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File attached:
'Analysis X-Ray Ligands 3rd Party ConfGen.xml'
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Description:
Source 1: SD file must be a 3-D SD file of the X-Ray Conformations
Source 2: SD file of all conformers generated from a 3rd Party algorithm
Result: Sorted list of conformers RMSD calculated from each XRay Conformer and the relative energies of each conformer to the X Ray Conf and the Lowest Energy Conf using the CONFIRM energy from CATALYST.
NOTES:
DS Components from DS 1.7 Release version (catConf and Analyze Poses)
All required parameters are listed on top level. Input SD Files, RMSD Atom Group (Heavy Atoms or All Atoms) and Output SD file.
Analysis data will be sent to HTML Viewers on your client.
Many files are written to Intermediate folders for your inspection
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System Requirements (versions tested on):
Discovery Studio 1.7.1
Pipeline Pilot 6.0.2
Tested on both Windows and Linux operating systems
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Software Licensing Requirements:
* DS Vis. Pro Enterprise OR (DS Vis. Pro and PP Enterprise server)
* DS Catalyst Conformation
* DS Analysis
* Pipeline Pilot Professional Client v 6.0.2
* Pipeline Pilot Component Collections: Chemistry, Generic. *** NOTE: protocols can be run on a server where only Discovery Studio 1.7 was installed -- all required component collections are embedded for runtime only access
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Installation Instructions:
1) Open Pipeline Pilot Client and change server if necessary
2) File -- Open -- browse for xml file
3) Save each protocol to your user folder: File -- Save Protocol) (browse for your username directory if necessary).
add required parameters of PP version to start protocol run
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Credits:
Amit Kulkarni - analysis components
Ragi Raghavan - review and case study to be published soon.
