MOLEonline: a web-based tool for analysing channels, tunnels
and pores (2025 update)

J 2025

MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update)

RAČEK, Tomáš; Dušan VEĽKÝ; Gabriela BUČEKOVÁ; Ondřej SCHINDLER; Ivana HUTAŘOVÁ VAŘEKOVÁ et al.

Základní údaje

Originální název

MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update)

Autoři

RAČEK, Tomáš; Dušan VEĽKÝ ; Gabriela BUČEKOVÁ ; Ondřej SCHINDLER; Ivana HUTAŘOVÁ VAŘEKOVÁ ; Anna ŠPAČKOVÁ; Václav BAZGIER; Karel BERKA a Radka SVOBODOVÁ

Vydání

Bioinformatics, Oxford University Press, 2025, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

30101 Human genetics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.400 v roce 2024

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14740/25:00141978

Organizační jednotka

Středoevropský technologický institut

Klíčová slova anglicky

Computational Biology; Databases; Protein; Internet; Protein Conformation; Proteins; Software; User-Computer Interface

Štítky

143160, CF BioData, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 14. 3. 2026 22:44, Mgr. Eva Dubská

Anotace

V originále

MOLEonline is an interactive, web-based tool designed to detect and analyse channels (pores and tunnels) within protein structures. The latest version of MOLEonline addresses the limitations of its predecessor by integrating the Mol* viewer for visualisation and offering a streamlined, fully interactive user experience. The new features include colouring tunnels in the 3D viewer based on their physicochemical properties. A 2D representation of the protein structure and calculated tunnels is generated using 2DProts. Users can now store tunnels directly in the mmCIF file format, facilitating sharing via the community-standard FAIR format for structural data. In addition, the ability to store and load computation settings ensures the reproducibility of tunnel computation results. Integration with the ChannelsDB 2.0 database allows users to access precomputed tunnels.

Návaznosti

GM22-30571M, projekt VaV

Název: Cell*: webová platforma pro vizualizaci, modelování a dynamiku organelových a buněčných struktur (Akronym: Cell*)

Investor: Grantová agentura ČR, Cell*: a web platform for visualization, modelling and dynamics of organelle- and cell-sized structures

LM2023055, projekt VaV

Název: Česká národní infrastruktura pro biologická data

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, ELIXIR-CZ: Česká národní infrastruktura pro biologická data

90254, velká výzkumná infrastruktura

Název: e-INFRA CZ II

Citovat

RAČEK, Tomáš; Dušan VEĽKÝ; Gabriela BUČEKOVÁ; Ondřej SCHINDLER; Ivana HUTAŘOVÁ VAŘEKOVÁ; Anna ŠPAČKOVÁ; Václav BAZGIER; Karel BERKA a Radka SVOBODOVÁ. MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update). Bioinformatics. Oxford University Press, 2025, roč. 41, č. 9, s. "btaf486", 5 s. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btaf486.

@article{2517192,
   author = {Raček, Tomáš and Veľký, Dušan and Bučeková, Gabriela and Schindler, Ondřej and Hutařová Vařeková, Ivana and Špačková, Anna and Bazgier, Václav and Berka, Karel and Svobodová, Radka},
   article_number = {9},
   doi = {https://doi.org/10.1093/bioinformatics/btaf486},
   keywords = {Computational Biology; Databases; Protein; Internet; Protein Conformation; Proteins; Software; User-Computer Interface},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update)},
   url = {https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf486/8246808},
   volume = {41},
   year = {2025}
}

TY  - JOUR
ID  - 2517192
AU  - Raček, Tomáš - Veľký, Dušan - Bučeková, Gabriela - Schindler, Ondřej - Hutařová Vařeková, Ivana - Špačková, Anna - Bazgier, Václav - Berka, Karel - Svobodová, Radka
PY  - 2025
TI  - MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update)
JF  - Bioinformatics
VL  - 41
IS  - 9
SP  - "btaf486"
EP  - "btaf486"
PB  - Oxford University Press
SN  - 13674803
KW  - Computational Biology
KW  - Databases
KW  - Protein
KW  - Internet
KW  - Protein Conformation
KW  - Proteins
KW  - Software
KW  - User-Computer Interface
UR  - https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaf486/8246808
N2  - MOLEonline is an interactive, web-based tool designed to detect and analyse channels (pores and tunnels) within protein structures. The latest version of MOLEonline addresses the limitations of its predecessor by integrating the Mol* viewer for visualisation and offering a streamlined, fully interactive user experience. The new features include colouring tunnels in the 3D viewer based on their physicochemical properties. A 2D representation of the protein structure and calculated tunnels is generated using 2DProts. Users can now store tunnels directly in the mmCIF file format, facilitating sharing via the community-standard FAIR format for structural data. In addition, the ability to store and load computation settings ensures the reproducibility of tunnel computation results. Integration with the ChannelsDB 2.0 database allows users to access precomputed tunnels.
ER  -

RAČEK, Tomáš; Dušan VEĽKÝ; Gabriela BUČEKOVÁ; Ondřej SCHINDLER; Ivana HUTAŘOVÁ VAŘEKOVÁ; Anna ŠPAČKOVÁ; Václav BAZGIER; Karel BERKA a Radka SVOBODOVÁ. MOLEonline: a web-based tool for analysing channels, tunnels and pores (2025 update). \textit{Bioinformatics}. Oxford University Press, 2025, roč.~41, č.~9, s.~''btaf486'', 5 s. ISSN~1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btaf486.

Přehled o publikaci