Is there any command-line methodology to construct a QSAR model for an alignment generated by a third party program, without doing hypothesis creation by Phase?

Yes. you can use $SCHRODINGER/phase_qsar. In addition to the aligned structures, you will have to set up a keyword/value pair input file for the job. Please contact help@schrodinger.com for a set of example files that can be used for guidance in setting up the job.

This type of job can also be run from Maestro: Applications → Phase → Individual QSAR Model.

Keywords: Phase, QSAR, existing alignment, Maestro

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