Analysis and Visualization of Protein Channels, Tunnels, and
Pores with MOLEonline and ChannelsDB 2.0

C 2024

Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0

ŠPAČKOVÁ, Anna; Václav BAZGIER; Tomáš RAČEK; David SEHNAL; Radka SVOBODOVÁ et al.

Základní údaje

Originální název

Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0

Autoři

ŠPAČKOVÁ, Anna; Václav BAZGIER; Tomáš RAČEK; David SEHNAL; Radka SVOBODOVÁ a Karel BERKA

Vydání

1. vyd. New York, Protein Bioinformatics, od s. 219-233, 15 s. Methods in Molecular Biology 2836, 2024

Nakladatel

Humana Press

Další údaje

Jazyk

angličtina

Typ výsledku

Kapitola resp. kapitoly v odborné knize

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

tištěná verze "print"

Odkazy

URL

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/24:00138961

Organizační jednotka

Přírodovědecká fakulta

ISBN

978-1-0716-4006-7

DOI

https://doi.org/10.1007/978-1-0716-4007-4_12

EID Scopus

2-s2.0-85198607054

Klíčová slova anglicky

Biomacromolecule; mmCIF; PDB; Physicochemical properties; Pore; Protein; Residues; Tunnel; Visualization; Voronoi; Channel

Štítky

143160, CF BioData, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 3. 3. 2025 15:54, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

Channels, tunnels, and pores serve as pathways for the transport of molecules and ions through protein structures, thus participating to their functions. MOLEonline (https://mole.upol.cz) is an interactive web-based tool with enhanced capabilities for detecting and characterizing channels, tunnels, and pores within protein structures. MOLEonline has two distinct calculation modes for analysis of channel and tunnels or transmembrane pores. This application gives researchers rich analytical insights into channel detection, structural characterization, and physicochemical properties. ChannelsDB 2.0 (https://channelsdb2.biodata.ceitec.cz/) is a comprehensive database that offers information on the location, geometry, and physicochemical characteristics of tunnels and pores within macromolecular structures deposited in Protein Data Bank and AlphaFill databases. These tunnels are sourced from manual deposition from literature and automatic detection using software tools MOLE and CAVER. MOLEonline and ChannelsDB visualization is powered by the LiteMol Viewer and Mol* viewer, ensuring a user-friendly workspace. This chapter provides an overview of user applications and usage.

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

Citovat

ŠPAČKOVÁ, Anna; Václav BAZGIER; Tomáš RAČEK; David SEHNAL; Radka SVOBODOVÁ a Karel BERKA. Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0. In Lisacek, Frédérique. Protein Bioinformatics. 1. vyd. New York: Humana Press, 2024, s. 219-233. Methods in Molecular Biology 2836. ISBN 978-1-0716-4006-7. Dostupné z: https://doi.org/10.1007/978-1-0716-4007-4_12.

@inbook{2481329,
   author = {Špačková, Anna and Bazgier, Václav and Raček, Tomáš and Sehnal, David and Svobodová, Radka and Berka, Karel},
   address = {New York},
   booktitle = {Protein Bioinformatics},
   doi = {https://doi.org/10.1007/978-1-0716-4007-4_12},
   edition = {1},
   editor = {Lisacek, Frédérique},
   keywords = {Biomacromolecule; mmCIF; PDB; Physicochemical properties; Pore; Protein; Residues; Tunnel; Visualization; Voronoi; Channel},
   howpublished = {tištěná verze "print"},
   language = {eng},
   location = {New York},
   isbn = {978-1-0716-4006-7},
   pages = {219-233},
   publisher = {Humana Press},
   title = {Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0},
   url = {https://doi.org/10.1007/978-1-0716-4007-4_12},
   year = {2024}
}

TY  - CHAP
ID  - 2481329
AU  - Špačková, Anna - Bazgier, Václav - Raček, Tomáš - Sehnal, David - Svobodová, Radka - Berka, Karel
PY  - 2024
TI  - Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0
VL  - Methods in Molecular Biology 2836
PB  - Humana Press
CY  - New York
SN  - 9781071640067
KW  - Biomacromolecule
KW  - mmCIF
KW  - PDB
KW  - Physicochemical properties
KW  - Pore
KW  - Protein
KW  - Residues
KW  - Tunnel
KW  - Visualization
KW  - Voronoi
KW  - Channel
UR  - https://doi.org/10.1007/978-1-0716-4007-4_12
N2  - Channels, tunnels, and pores serve as pathways for the transport of molecules and ions through protein structures, thus participating to their functions. MOLEonline (https://mole.upol.cz) is an interactive web-based tool with enhanced capabilities for detecting and characterizing channels, tunnels, and pores within protein structures. MOLEonline has two distinct calculation modes for analysis of channel and tunnels or transmembrane pores. This application gives researchers rich analytical insights into channel detection, structural characterization, and physicochemical properties. ChannelsDB 2.0 (https://channelsdb2.biodata.ceitec.cz/) is a comprehensive database that offers information on the location, geometry, and physicochemical characteristics of tunnels and pores within macromolecular structures deposited in Protein Data Bank and AlphaFill databases. These tunnels are sourced from manual deposition from literature and automatic detection using software tools MOLE and CAVER. MOLEonline and ChannelsDB visualization is powered by the LiteMol Viewer and Mol* viewer, ensuring a user-friendly workspace. This chapter provides an overview of user applications and usage.
ER  -

ŠPAČKOVÁ, Anna; Václav BAZGIER; Tomáš RAČEK; David SEHNAL; Radka SVOBODOVÁ a Karel BERKA. Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0. In Lisacek, Frédérique. \textit{Protein Bioinformatics}. 1. vyd. New York: Humana Press, 2024, s.~219-233. Methods in Molecular Biology 2836. ISBN~978-1-0716-4006-7. Dostupné z: https://doi.org/10.1007/978-1-0716-4007-4\_{}12.

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