💻 Usage

Ensemblify offers several main modules, all of which can be accessed either through the command line or from inside a Python script/Jupyter Notebook.

• modelling module: create full-length protein structures by fusing PDB structures of folded protein domains with disordered regions.

• generation module: generate a conformational ensemble for your protein of interest.

• conversion module: convert your generated .pdb structures into a single .xtc trajectory file, facilitating ensemble storage and analysis.

• analysis module: create an interactive graphical dashboard displaying structural information calculated from the conformational ensemble of your protein of interest.

• reweighting module: use experimental SAXS data to reweight your conformational ensemble following the Bayesian/Maximum Entropy method.

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Ensemblify also offers minor modules that can be accessed through the command line or from inside a Python script/Jupyter Notebook.

• clash_checking module: check previously generated ensembles (even ones generated not using Ensemblify) for steric clashes, outputting detailed reports.