FRASE-bot is a collection of protocols developed in Pipeline Pilot, a data processing software featuring its own programming language (Pilot Script). Pipeline Pilot requires a commercial license from 3DS Biovia (www.3ds.com/products-services/biovia/). Pipeline Pilot is a client-server software; client can be run on a Windows computer and server either on Windows or Linux (3DS Biovia provides detailed instructions on system requirements and installation ).

Once Pipeline Pilot installed, the .ppxml files can be imported and executed. The FRASE-bot workflow steps are separate protocols numbered from 1 to 9. The protocol components have intuitive titles and the Pilot script code within custom manipulators is commented.

The input/output files for each component are provided as Mendeley data at https://data.mendeley.com/datasets/9yn47cy5jv/1

The fitness scores for hit FRASEs are calculated using the Python code predict.py. The command syntax is "predict.py input.txt", where input.txt is generated by the Pipeline Pilot protocol "07-FRASE-bot - Calculate descriptors for scoring.ppxml" (it has a suffix "-aconv"). "Predict.py" loads the neural network model from the file "FRASE_model.h5" - this file must be placed in the same folder as "predict.py". The Conda environment for running the predictions can be loaded from specs.txt.