Dear Colleagues:
Please find below two protocols that have been built where a user can compare and evaluate the performance of four conformational model generation algorithms available from Accelrys: CONFIRM/BEST, CONFIRM/FAST, CAESAR, PipelinePilot Conformer Generation.
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Attached Files:
** 'Compare Conf Generators PP.xml'
ready for running natively in Pipeline Pilot Professional Client
** 'Compare Conf Generators DS.xml'
ready for running natively in Discovery Studio 1.7 Client
** 'five-xray-ligs.sd'
sample file of 5 xray conformers
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Description:
DS 1.7 Component Collection for CATALYST
Source SD file must be a 3-D SD file of the X-Ray Conformations
Result: Sorted list of conformers from each catConf method with 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. Analysis data will be sent to HTML Viewers on your client.
Notes:
DS Components from DS 1.7 Release version (catConf and Analyze Poses)
All required parameters are listed on top level. SD File, RMSD Atom Group (Heavy Atoms or All Atoms), Number of Conformers. User defined filters for Random Percent and Rotatable bonds are available.
Max No. of Molecules -- this is the parameter for the input SD file. If you want all input molecules, leave it blank and make sure Random Percent filter is set to False.
Many files are written to Intermediate folders for your inspection
Additional Details on DS ready protocol:
Sorted list of conformers from each conformer generation method with 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. Analysis data is printed on the Report.htm summary. Per molecule analysis data present txt files in Output directory.
Viewing the Results:
From our experience, we have found an extremely useful way to visualize the output is using Discovery Studio 1.7 by reading in the output SD file into a Table Browser and using the Group By and Represent By operations to easily select a series of conformers in a 3D view
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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, Advanced 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 files
3) Save each protocol to your user folder: File -- Save Protocol) (browse for your username directory if necessary).
add required parameters of PP version
for DS version, open Discovery Studio 1.7 and browse for "Compare Conf Generators DS" in your Protocols tab > Username folder.
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Credits:
Amit Kulkarni - analysis components
Ragi Raghavan - review and case study to be published soon
