ValTrendsDB: Database of biomacromolecular structure validation trends

HORSKÝ, Vladimír, Veronika BENDOVÁ, Dominik TOUŠEK, Jaroslav KOČA and Radka SVOBODOVÁ VAŘEKOVÁ. ValTrendsDB: Database of biomacromolecular structure validation trends. 2019.

Basic information

• Original name: ValTrendsDB: Database of biomacromolecular structure validation trends
• Authors: HORSKÝ, Vladimír (203 Czech Republic, guarantor, belonging to the institution), Veronika BENDOVÁ (203 Czech Republic, belonging to the institution), Dominik TOUŠEK (203 Czech Republic, belonging to the institution), Jaroslav KOČA (203 Czech Republic, belonging to the institution) and Radka SVOBODOVÁ VAŘEKOVÁ (203 Czech Republic, belonging to the institution).
• Edition: 2019.

Other information

• Original language: English
• Type of outcome: Software
• Field of Study: 10608 Biochemistry and molecular biology
• Country of publisher: Czech Republic
• Confidentiality degree: is not subject to a state or trade secret
• WWW: URL
• RIV identification code: RIV/00216224:14740/19:00110338
• Organization unit: Central European Institute of Technology
• Keywords in English: PDB; PDBe; Protein Data Bank; three-dimensional macromolecular structure; validation; wwPDB validation pipeline; ligands; ValTrendsDB; database; trends in quality; visualization; statistical analysis; C++; Qt SDK; JavaScript; d3.js; Metro UI
• Technical parameters: ValTrendsDB is updated weekly, and is freely accessible at http://ncbr.muni.cz/ValTrendsDB. The web interface was implemented in JavaScript using the d3.js library as well as the Metro UI design elements. The database back-end was implemented in C++ using the Qt SDK. Communication between the web interface and the back-end is carried out via local HTTPS communication on the server. Responses of the back-end are buffered using the Apache server.
• Tags: rivok
• Tags: International impact, Reviewed

Abstract

Structures in PDB tend to contain errors. This is a very serious issue for authors that rely on such potentially problematic data. The community of structural biologists develops validation methods as countermeasures, which are also included in the PDB deposition system. But how are these validation efforts influencing the structure quality of subsequently published data? Which quality aspects are improving, and which remain problematic? We developed ValTrendsDB, a database that provides the results of an extensive exploratory analysis of relationships between quality criteria, size and metadata of biomacromolecules. Key input data are sourced from PDB. The discovered trends are presented via precomputed information-rich plots. ValTrendsDB also supports the visualization of a set of user-defined structures on top of general quality trends. Therefore, ValTrendsDB enables users to see the quality of structures published by selected author, laboratory or journal, discover quality outliers, etc.

Links

• ATCZ40, interní kód MU: Name: Creating synergies between research infrastructures to stimulate innovation in the cross-border region (Acronym: RIAT-CZ)

Investor: Ministry for Regional Development of the CR

• EF16_013/0001777, research and development project: Name: ELIXIR-CZ: Budování kapacit
• 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

• LQ1601, research and development project: Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

• MUNI/A/1503/2018, interní kód MU: Name: Matematické statistické modelování 3 (Acronym: MaStaMo3)

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)