Large-scale comparison between the diffraction-component precision indexes favors Cruickshanks Rfree function Scientific paper

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Sorin Avram
Cristian Neanu


This study aims to provide a first large-scale comparison between the various diffraction-component precision index (DPI) equations, assess the applic­ability of the parameter, and make recommendations on DPI com­putation. The DPI 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 DPI equations based on R and Rfree in order to calculate DPI 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 R and Rfree DPI variations. Computations of 143070 X-ray structures indicate that Rfree-based DPI equations apply to 30 % more pro­tein structures compared to R-based DPI equations, with Cruickshank Rfree-
-based DPI (CRF) exceeding the number of successful Blows Rfree-based DPI (BRF) computations. Although our results indicate that, in general, the resol­utions < 2 Å assure consistency among the various DPIs computations (differ­ences <0.05 Å), we recommend the use of CRF DPI because of its wider applicability.


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S. Avram and C. Neanu, “Large-scale comparison between the diffraction-component precision indexes favors Cruickshanks Rfree function: Scientific paper”, J. Serb. Chem. Soc., vol. 87, no. 3, pp. 321–330, Nov. 2021.
Theoretical Chemistry


P. Willett, WIREs Comput. Mol. Sci. 1 (2011) 10 (

G. Sliwoski, S. Kothiwale, J. Meiler, E.W. Lowe Jr., Pharmacol. Rev. 66 (2014) 334 (

D. M. Popović, S. D. Zarić, B. Rabenstein, E.-W. Knapp, J. Am. Chem. Soc. 25 (2001) 6040 (

S. Zarić, D. Popović, E.-W. Knapp, Chem. Eur. J. 6 (2000) 3935 (;2-J)

G. L. Warren, T. D. Do, B. P. Kelley, A. Nicholls, S. D. Warren, Drug Discov. Today 17 (2012) 1270 (

H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, Nucleic Acids Res. 28 (2000) 235 (

S. K. Burley, H. M. Berman, C. Bhikadiya, C. Bi, L. Chen, L. Di Costanzo, C. Christie, K. Dalenberg, J. M. Duarte, S. Dutta, Z. Feng, S. Ghosh, D. S. Goodsell, R. K. Green, V. Guranovic, D. Guzenko, B. P. Hudson, T. Kalro, Y. Liang, R. Lowe, H. Namkoong, E. Peisach, I. Periskova, A. Prlic, C. Randle, A. Rose, P. Rose, R. Sala, M. Sekharan, C. Shao, L. Tan, Y. P. Tao, Y. Valasatava, M. Voigt, J. Westbrook, J. Woo, H. Yang, J. Young, M. Zhuravleva, C. Zardecki, Nucleic Acids Res. 47 (2019) D464 (

H. Berman, K. Henrick, H. Nakamura, Nat. Struct. Biol. 10 (2003) 980 (

H. Berman, K. Henrick, H. Nakamura, J. L. Markley, Nucleic Acids Res. 35 (2007) D301 (

wwPDB consortium, Nucleic Acids Res. 47 (2019) D520 (

M. J. Domagalski, H. Zheng, M. D. Zimmerman, Z. Dauter, A. Wlodawer, W. Minor, Structural Genomics. Methods in Molecular Biology, Vol. 1091, Humana Press, Totowa, NJ, 2014, p. 297 (

N. V. Zukang Feng, Luigi Di Costanzo, D. S. Goodsell, J. D. Westbrook, S. K. Burley, C. Zardecki, Data Sci. J. 19 (2020) 25 (

A. T. Brunger, Nature 355 (1992) 472 (

D .W. Cruickshank, Acta Cryst., D 55 (1999) 1108 (

D .M. Blow, Acta Crystallogr., D 58 (2002) 792 (

P. C. Hawkins, A. G. Skillman, G. L. Warren, B. A. Ellingson, M. T. Stahl, J. Chem. Inf. Model. 50 (2010) 572 (

P. C. Hawkins, G. L. Warren, A. G. Skillman, A. Nicholls, J. Comput.-Aided Mol. Des. 22 (2008) 179 (

S. I. Avram, L. Crisan, L. M. Pacureanu, A. Bora, E. Seclaman, M. Balint, L. G. Kurunczi, Med. Chem. Res. 22 (2012) 3589 (

K. S. D. Kumar, M. Gurusaran, S. N. Satheesh, P. Radha, S. Pavithra, K. P. S. Thulaa Tharshan, J. R. Helliwell, K. Sekar, J. Appl. Crystallogr. 48 (2015) 939 (

M. Gurusaran, M. Shankar, R. Nagarajan, J. R. Helliwell, K. Sekar, IUCrJ 1 (2014) 74 (

J. Goto, R. Kataoka, N. Hirayama, J. Med. Chem. 47 (2004) 6804 (

L. Halip, S. Avram, C. Neanu, Struct. Chem. 32 (2021) 1693 (

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