Figure 1.

Scheme of the RNA-Puzzles toolkit. The toolkit is composed of three parts: tools for validation and standardization of PDB structure files, tools for analyzing the models, and the dataset of standardized submissions to the RNA-Puzzle. The user can start an analysis with single or multiple models. The first step is to standardize the formatting of analyzed structural models. Then, the user can run an analysis for a single model, such as Clash Score evaluation or base pair identification using various methods; or, for multiple models, various comparison methods are implemented. The tools can be accessed via command-line or Jupyter. The toolkit can be also executed as a Docker image that can be easily used.