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A series of PDB related databases for everyday needs.

ABSTRACT: The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials from the other systems. PDB_REDO holds re-refined, and often improved, copies of all structures solved by X-ray. WHY_NOT summarizes why certain files could not be produced. All these systems are updated weekly. The data sets can be used for the analysis of properties of protein structures in areas ranging from structural genomics, to cancer biology and protein design.

SUBMITTER: Joosten RP

PROVIDER: S-EPMC3013697 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature

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A series of PDB related databases for everyday needs.

Joosten Robbie P RP te Beek Tim A H TA Krieger Elmar E Hekkelman Maarten L ML Hooft Rob W W RW Schneider Reinhard R Sander Chris C Vriend Gert G

Nucleic acids research 20101111 Database issue

The Protein Data Bank (PDB) is the world-wide repository of macromolecular structure information. We present a series of databases that run parallel to the PDB. Each database holds one entry, if possible, for each PDB entry. DSSP holds the secondary structure of the proteins. PDBREPORT holds reports on the structure quality and lists errors. HSSP holds a multiple sequence alignment for all proteins. The PDBFINDER holds easy to parse summaries of the PDB file content, augmented with essentials fr ...[more]

PMID: 21071423

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Project description:IntroductionUnmet health-related social needs (HRSN) are among the drivers of disparities in morbidity and mortality during public health emergencies such as the novel coronavirus 2019 (Covid-19) pandemic. Although emergency departments (ED) see a high volume of patients with HRSN, ED providers have limited time to complete detailed assessments of patients' HRSN and are not always able to provide up-to-date and comprehensive information to patients on available community resources. Electronic, geographically indexed resource database systems have the potential to provide an efficient way for emergency physicians to rapidly identify community resources in settings where immediate social work consultation is not accessible.MethodsWe conducted a systematic review of papers examining the use of geographically indexed resource database systems in healthcare to better understand how these services can be used in emergency care. We then conducted simulated, standardized searches using two nationally available databases (211 and Aunt Bertha), applied to a single metropolitan area (Boston).ResultsOur systematic review found that most public health and screening interventions using nationally available databases have focused on chronic care needs. A small subset of publications demonstrated that these databases were mobilized during disasters to successfully aid vulnerable populations during Hurricanes Katrina and Rita. A total of 408 standardized searches were conducted to identify community resources related to four domains of social needs (food, transportation, housing, and utilities). Although 99% of the resources identified by both databases were relevant to the search domains queried, a significant proportion of the resources identified by each database were restricted to a specific demographic (eg, veterans).ConclusionOur findings demonstrate that geographically indexed referral databases may be an effective tool to help ED providers connect patients to nearby community resources during public health emergencies. We recommend that EDs select a referral database based on the greatest number of resources that are not demographically restricted.

Project description:Metaphors are often used to describe cancer experiences (e.g., battle, journey). Few studies explore how social threats (e.g., discrimination) shape metaphor preferences. We examined the relationship between discrimination and preferences for cancer battle metaphors (i.e., concrete, action-based) versus journey metaphors (i.e., open-ended, reflective) and mediating effects of needs for personal significance and cognitive closure. We also stratified the analysis when discrimination was/was not attributed to race and by racial/ethnic group. Four-hundred twenty-seven U.S. participants completed an online survey. Items included everyday discrimination, need for personal significance, need for cognitive closure, and preference for cancer scenarios using battle or journey metaphors. Multigroup structural equation modeling examined: serial mediation (i.e., discrimination predicting metaphor preference via needs for personal significance and cognitive closure) stratified by discrimination attribution; and single mediation (i.e., discrimination predicting need for cognitive closure via need for personal significance) stratified by racial/ethnic group. Discrimination was associated with battle metaphor preferences through serial mediation when discrimination was not attributed to race (β = 0.02, 95% CI [0.01,0.05]). Discrimination was directly associated with journey metaphor preferences (β = -0.20, 95% CI [-0.37,-0.06]) and the serial mediation was nonsignificant when discrimination was attributed to race. The single mediation model varied across racial/ethnic groups and was strongest for Non-Hispanic White participants (β = 0.17, 95% CI [0.07,0.30]). Discrimination may shape cancer metaphor preferences through needs for personal significance and cognitive closure, yet these relationships differ based on whether discrimination is attributed to race and racial/ethnic group. Given that the U.S. health system often focuses on battle metaphors when framing cancer treatment and screenings, individuals who prefer journey metaphors (i.e., those who experienced more frequent racial discrimination in the present study) may experience a systematic disadvantage in cancer communication. A more careful consideration of cultural, racial, and ethnic differences in metaphor use may be a crucial step towards reducing cancer disparities.

Dataset Information

A series of PDB related databases for everyday needs.

Publications

A series of PDB related databases for everyday needs.

Similar Datasets

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