Visualization and Analysis of Protein Structures with LiteMol Suite

SEHNAL, David, Radka SVOBODOVÁ, K. BERKA, Lukáš PRAVDA, Adam MIDLIK and Jaroslav KOČA. Visualization and Analysis of Protein Structures with LiteMol Suite. Online. In STRUCTURAL BIOINFORMATICS: METHODS AND PROTOCOLS. TOTOWA: HUMANA PRESS INC, 2020, p. 1-13. 2112. ISBN 978-1-0716-0270-6. Available from: https://dx.doi.org/10.1007/978-1-0716-0270-6_1.

Basic information

• Original name: Visualization and Analysis of Protein Structures with LiteMol Suite
• Authors: SEHNAL, David (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ (203 Czech Republic, guarantor, belonging to the institution), K. BERKA, Lukáš PRAVDA (203 Czech Republic, belonging to the institution), Adam MIDLIK (703 Slovakia, belonging to the institution) and Jaroslav KOČA (203 Czech Republic, belonging to the institution).
• Edition: TOTOWA, STRUCTURAL BIOINFORMATICS: METHODS AND PROTOCOLS, p. 1-13, 13 pp. 2112, 2020.
• Publisher: HUMANA PRESS INC

Other information

• Original language: English
• Type of outcome: Chapter(s) of a specialized book
• Field of Study: 10608 Biochemistry and molecular biology
• Country of publisher: United States of America
• Confidentiality degree: is not subject to a state or trade secret
• Publication form: electronic version available online
• WWW: URL
• RIV identification code: RIV/00216224:14740/20:00122562
• Organization unit: Central European Institute of Technology
• ISBN: 978-1-0716-0270-6
• Doi: http://dx.doi.org/10.1007/978-1-0716-0270-6_1
• UT WoS: 000680164300002
• Keywords in English: Protein visualization; Atom selection; Validation report; Ligand representation; Electron density
• Tags: rivok
• Tags: International impact, Reviewed

Abstract

LiteMol suite is an innovative solution that enables near-instant delivery of model and experimental biomacromolecular structural data, providing users with an interactive and responsive experience in all modern web browsers and mobile devices. LiteMol suite is a combination of data delivery services (CoordinateServer and DensityServer), compression format (BinaryCIF), and a molecular viewer (LiteMol Viewer). The LiteMol suite is integrated into Protein Data Bank in Europe (PDBe) and other life science web applications (e.g., UniProt, Ensemble, SIB, and CNRS services), it is freely available at https://litemol.org, and its source code is available via GitHub. LiteMol suite provides advanced functionality (annotations and their visualization, powerful selection features), and this chapter will describe their use for visual inspection of protein structures.

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

• 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)