@article{Avram_Neanu_2021, place={Belgrade, Serbia}, title={Large-scale comparison between the diffraction-component precision indexes favors Cruickshanks Rfree function: Scientific paper}, volume={87}, url={https://www.shd-pub.org.rs/index.php/JSCS/article/view/10775}, DOI={10.2298/JSC200518076A}, abstractNote={<p>This study aims to provide a first large-scale comparison between the various diffraction-component precision index (<em>DPI</em>) equations, assess the applic­ability of the parameter, and make recommendations on <em>DPI</em> com­putation. The <em>DPI</em> estimates the average accuracy of the atomic coordinates obtained by the struc­tural refinement of protein diffraction data, with applic­ation in crystal­lography and cheminformatics. Although, Cruickshank and Blow proposed <em>DPI</em> equations based on <em>R</em> and <em>R</em><sub>free</sub> in order to calculate <em>DPI</em> values, which remain scarcely employed in the quality assessment of the Pro­tein Data Base (PDB) files, due to the unclear data extraction protocols (to assign variables), the complex equations, the lack of extensive applicability studies and the limited access to automated computations. In order to address these shortcomings, the entire RCSB PDB database was evaluated using Cruickshanks and Blows <em>R</em> and <em>R</em><sub>free</sub> <em>DPI</em> variations. Computations of 143070 X-ray structures indicate that <em>R</em><sub>free</sub>-based <em>DPI</em> equations apply to 30 % more pro­tein structures compared to <em>R</em>-based <em>DPI</em> equations, with Cruickshank <em>R</em><sub>free</sub>-<br />-based <em>DPI</em> (<em>CR</em>F) exceeding the number of successful Blows <em>R</em><sub>free</sub>-based <em>DPI</em> (<em>BR</em>F) computations. Although our results indicate that, in general, the resol­utions < 2 Å assure consistency among the various <em>DPI</em>s computations (differ­ences <0.05 Å), we recommend the use of <em>CR</em>F <em>DPI</em> because of its wider applicability.</p>}, number={3}, journal={Journal of the Serbian Chemical Society}, author={Avram, Sorin and Neanu, Cristian}, year={2021}, month={Nov.}, pages={321–330} }