CoverView: clear atom-level visualization of electron density coverage of PDB structures to assist validation

CHARESHNEU, Aliaksei, David SEHNAL and Radka SVOBODOVÁ. CoverView: clear atom-level visualization of electron density coverage of PDB structures to assist validation. 2022.

Basic information

• Original name: CoverView: clear atom-level visualization of electron density coverage of PDB structures to assist validation
• Authors: CHARESHNEU, Aliaksei (112 Belarus, guarantor, belonging to the institution), David SEHNAL (203 Czech Republic, belonging to the institution) and Radka SVOBODOVÁ (203 Czech Republic, belonging to the institution).
• Edition: 2022.

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/00216224:14740/22:00124983
• Organization unit: Central European Institute of Technology
• Keywords in English: proteins; visualization; electron density; coverage; PDB
• Technical parameters: webová aplikace
• Tags: rivok

Abstract

A prototype of a web server allowing the users to clearly visualize the electron density coverage of a protein structure at the level of atoms. Consists of a sortable table with relevant information (title, assembly weight, total atoms, fraction of atoms covered, resolution high, R factor, R free) on a set of selected structures linked to pre-created Mol* sessions, where each structure is colored according to the electron density coverage of atoms (green – covered, red – not covered). The implementation is based on a Python library called gemmi.

Links

• LM2018131, 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