Worldwide Protein Data Bank validation information: usage and trends

SMART, Oliver S., Vladimír HORSKÝ, Swanand GORE, Radka SVOBODOVÁ VAŘEKOVÁ, Veronika BENDOVÁ, Gerard J. KLEYWEGT and Sameer VELANKAR. Worldwide Protein Data Bank validation information: usage and trends. Acta Crystallographica Section D. 2018, vol. 74, MAR, p. 237-244. ISSN 2059-7983. Available from: https://dx.doi.org/10.1107/S2059798318003303.

Basic information

• Original name: Worldwide Protein Data Bank validation information: usage and trends
• Authors: SMART, Oliver S. (826 United Kingdom of Great Britain and Northern Ireland), Vladimír HORSKÝ (203 Czech Republic, belonging to the institution), Swanand GORE (826 United Kingdom of Great Britain and Northern Ireland), Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, guarantor, belonging to the institution), Veronika BENDOVÁ (203 Czech Republic, belonging to the institution), Gerard J. KLEYWEGT (528 Netherlands) and Sameer VELANKAR (826 United Kingdom of Great Britain and Northern Ireland).
• Edition: Acta Crystallographica Section D, 2018, 2059-7983.

Other information

• Original language: English
• Type of outcome: Article in a journal
• Field of Study: 10608 Biochemistry and molecular biology
• Country of publisher: United Kingdom of Great Britain and Northern Ireland
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• Impact factor: Impact factor: 3.227
• RIV identification code: RIV/00216224:14740/18:00102378
• Organization unit: Central European Institute of Technology
• Doi: http://dx.doi.org/10.1107/S2059798318003303
• UT WoS: 000427362000007
• Keywords in English: PDB; Protein Data Bank; three-dimensional macromolecular structure; validation; quality control; X-ray crystallography; ValTrendsDB
• Tags: rivok
• Tags: International impact, Reviewed

Abstract

It is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. Additionally, ValTrendsDB database is presented: It provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

Links

• LM2015047, research and development project: Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

• MUNI/A/1204/2017, interní kód MU: Name: Matematické statistické modelování 2 (Acronym: MaStaMo2)

Investor: Masaryk University, Category A

• 676559, interní kód MU: Name: ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences (Acronym: ELIXIR-EXCELERATE)

Investor: European Union, RI Research Infrastructures (Excellent Science)