Dataset Information

ECOD: new developments in the evolutionary classification of domains.

ABSTRACT: Evolutionary Classification Of protein Domains (ECOD) (http://prodata.swmed.edu/ecod) comprehensively classifies protein with known spatial structures maintained by the Protein Data Bank (PDB) into evolutionary groups of protein domains. ECOD relies on a combination of automatic and manual weekly updates to achieve its high accuracy and coverage with a short update cycle. ECOD classifies the approximately 120 000 depositions of the PDB into more than 500 000 domains in ?3400 homologous groups. We show the performance of the weekly update pipeline since the release of ECOD, describe improvements to the ECOD website and available search options, and discuss novel structures and homologous groups that have been classified in the recent updates. Finally, we discuss the future directions of ECOD and further improvements planned for the hierarchy and update process.

SUBMITTER: Schaeffer RD

PROVIDER: S-EPMC5210594 | biostudies-literature | 2017 Jan

REPOSITORIES: biostudies-literature

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ECOD: new developments in the evolutionary classification of domains.

Schaeffer R Dustin RD Liao Yuxing Y Cheng Hua H Grishin Nick V NV

Nucleic acids research 20161129 D1

Evolutionary Classification Of protein Domains (ECOD) (http://prodata.swmed.edu/ecod) comprehensively classifies protein with known spatial structures maintained by the Protein Data Bank (PDB) into evolutionary groups of protein domains. ECOD relies on a combination of automatic and manual weekly updates to achieve its high accuracy and coverage with a short update cycle. ECOD classifies the approximately 120 000 depositions of the PDB into more than 500 000 domains in ∼3400 homologous groups. W ...[more]

PMID: 27899594

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Project description:Background and objectivesThe histopathologic classification for ANCA-associated GN distinguishes four classes on the basis of patterns of injury. In the original validation study, these classes were ordered by severity of kidney function loss as follows: focal, crescentic, mixed, and sclerotic. Subsequent validation studies disagreed on outcomes in the crescentic and mixed classes. This study, driven by the original investigators, provides several analyses in order to determine the current position of the histopathologic classification of ANCA-associated GN.Design, setting, participants, & measurementsA validation study was performed with newly collected data from 145 patients from ten centers worldwide, including an analysis of interobserver agreement on the histopathologic evaluation of the kidney biopsies. This study also included a meta-analysis on previous validation studies and a validation of the recently proposed ANCA kidney risk score.ResultsThe validation study showed that kidney failure at 10-year follow-up was significantly different between the histopathologic classes (P<0.001). Kidney failure at 10-year follow-up was 14% in the crescentic class versus 20% in the mixed class (P=0.98). In the meta-analysis, no significant difference in kidney failure was also observed when crescentic class was compared with mixed class (relative risk, 1.15; 95% confidence interval, 0.94 to 1.41). When we applied the ANCA kidney risk score to our cohort, kidney survival at 3 years was 100%, 96%, and 77% in the low-, medium-, and high-risk groups, respectively (P<0.001). These survival percentages are higher compared with the percentages in the original study.ConclusionsThe crescentic and mixed classes seem to have a similar prognosis, also after adjusting for differences in patient populations, treatment, and interobserver agreement. However, at this stage, we are not inclined to merge the crescentic and mixed classes because the reported confidence intervals do not exclude important differences in prognosis and because an important histopathologic distinction would be lost.

Dataset Information

ECOD: new developments in the evolutionary classification of domains.

Publications

ECOD: new developments in the evolutionary classification of domains.

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