2020
DOI: 10.1111/febs.15314
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On the evolution of the quality of macromolecular models in the PDB

Abstract: Crystallographic models of biological macromolecules have been ranked using the quality criteria associated with them in the Protein Data Bank (PDB). The outcomes of this quality analysis have been correlated with time and with the journals that published papers based on those models. The results show that the overall quality of PDB structures has substantially improved over the last ten years, but this period of progress was preceded by several years of stagnation or even depression. Moreover, the study shows… Show more

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Cited by 17 publications
(24 citation statements)
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“…Some aspects of this protocol are general in nature, and the exact values may be changed for a particular structure. The protocol and decisions made for each structure are based on our extensive experience in protein structure determination, [14][15][16] crystallographic software development, 17,18 published guidelines on structure refinement and structure quality, 7,19,20 and previous campaigns of PDB structure re-refinement 21,22 :…”
Section: Structure Correction Protocolmentioning
confidence: 99%
“…Some aspects of this protocol are general in nature, and the exact values may be changed for a particular structure. The protocol and decisions made for each structure are based on our extensive experience in protein structure determination, [14][15][16] crystallographic software development, 17,18 published guidelines on structure refinement and structure quality, 7,19,20 and previous campaigns of PDB structure re-refinement 21,22 :…”
Section: Structure Correction Protocolmentioning
confidence: 99%
“…Looking at the release dates for the PDB structures in our dataset (Figure 1), it can be observed that most structures with LDRs have been deposited in the last five years, suggesting that the improvements of crystallization techniques are allowing the growth of crystals of partially disordered or flexible proteins [25,26]. While the amount of structures deposited remains roughly stable in the last years, a steady increment of PDB files with LDRs can be seen.…”
Section: Quality Of Structures With Disordered Regionsmentioning
confidence: 90%
“…Structure quality metrics reported in the PDB [ 27 ] were assigned to each X-ray structure by using the recently published dataset by Brzezinski et al [ 25 ], available at . Six key validation metrics were used to measure the overall structure quality: Resolution, R-free, clashscore, Ramachandran outliers, rotamer outliers and RSRZ outliers (normalized real-space R-factor).…”
Section: Methodsmentioning
confidence: 99%
See 1 more Smart Citation
“…Ever since the conception of Protein Data Bank (PDB) 1,2 and GenBank, 3,4 open access to standardised and searchable pools of experimental data has revolutionized scientific research. Constantly growing and improving in fidelity due to collaborative effort, [5][6][7][8] the now hundreds of databanks 9 fuel the data-driven development of biomolecular structure determination, 10 refinement, 11 prediction, 12 and design 13 approaches, as well as development of drugs, 14,15 materials, 16,17 and more. 18,19 It is clear that open data enables scientific progress that is far beyond the resources of a single research group or institute.…”
Section: Introductionmentioning
confidence: 99%