Reproducible PDB analysis accompanying the paper "On the evolution of the quality of crystallographic models in the PDB".
Notice: The PDBj has changed its database schema since the publication. For those wanting to run similar queries on the current version of the PDBj, please take a look at the PDB analysis_updated_2021.ipynb. Do have in mind, however, that since June 2021 the PDBj is switching to a new validation report format and some of the validation are currently missing. The situation will be fixed upon the recalculation of all validation reports by wwPDB, presumably sometime by the end of 2021. For these reasons, temporarily it might be difficult to get all the data needed for an up-to-date analysis. If you are OK with data up to 2019, you can you the original results from the results_original folder.
The repository contains the input PDB metadata, reproducible experimental source code in the form of a Jupyter notebook, and detailed results of the analyses discussed in "On the evolution of the quality of crystallographic models in the PDB." by Brzezinski et al. The repository is divided into the following folders:
- the root folder contains the source code in the form of a Jupyter notebook, to start the analysis run the
PDB analysis.ipynbnotebook; datacontains datasets with information about publications and structure quality connected with each PDB deposit;results_originaldetailed tabular results (in CSV format) corresponding to different parts of the analysis.
To run the experiments the following software has to be installed:
- experiments were run using Python 3.7.3;
- a complete list of modules if available in
requirements.txtin the root folder.
If you have trouble reproducing the experiments or have any comments/suggestions, feel free to write at dariusz.brzezinski (at) cs.put.poznan.pl