PDBImages: a command-line tool for automated macromolecular
structure visualization

J 2023

PDBImages: a command-line tool for automated macromolecular structure visualization

MIDLIK, Adam; Sreenath NAIR; Stephen ANYANGO; Mandar DESHPANDE; David SEHNAL et al.

Základní údaje

Originální název

PDBImages: a command-line tool for automated macromolecular structure visualization

Autoři

MIDLIK, Adam; Sreenath NAIR; Stephen ANYANGO; Mandar DESHPANDE; David SEHNAL; Mihaly VARADI a Sameer VELANKAR

Vydání

Bioinformatics, Oxford, Oxford University Press, 2023, 1367-4803

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.400

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/23:00134386

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

biomacromolecules; organelle- and cell-sized models; PDBImages; open-source; visualization; databases; software; 3D structure; bioinformatics

Štítky

143160, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 4. 3. 2024 08:37, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to generate high-quality images for PDB and AlphaFold DB models. Its unique ability to render and save images directly to files in a browserless mode sets it apart, offering users a streamlined, automated process for macromolecular structure visualization. Here, we detail the implementation of PDBImages, enumerating its diverse image types, and elaborating on its user-friendly setup. This powerful tool opens a new gateway for researchers to visualize, analyse, and share their work, fostering a deeper understanding of bioinformatics.

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

Citovat

MIDLIK, Adam; Sreenath NAIR; Stephen ANYANGO; Mandar DESHPANDE; David SEHNAL; Mihaly VARADI a Sameer VELANKAR. PDBImages: a command-line tool for automated macromolecular structure visualization. Bioinformatics. Oxford: Oxford University Press, 2023, roč. 39, č. 12, s. 1-4. ISSN 1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btad744.

@article{2364582,
   author = {Midlik, Adam and Nair, Sreenath and Anyango, Stephen and Deshpande, Mandar and Sehnal, David and Varadi, Mihaly and Velankar, Sameer},
   article_location = {Oxford},
   article_number = {12},
   doi = {https://doi.org/10.1093/bioinformatics/btad744},
   keywords = {biomacromolecules; organelle- and cell-sized models; PDBImages; open-source; visualization; databases; software; 3D structure; bioinformatics},
   language = {eng},
   issn = {1367-4803},
   journal = {Bioinformatics},
   title = {PDBImages: a command-line tool for automated macromolecular structure visualization},
   url = {https://academic.oup.com/bioinformatics/article/39/12/btad744/7470737},
   volume = {39},
   year = {2023}
}

TY  - JOUR
ID  - 2364582
AU  - Midlik, Adam - Nair, Sreenath - Anyango, Stephen - Deshpande, Mandar - Sehnal, David - Varadi, Mihaly - Velankar, Sameer
PY  - 2023
TI  - PDBImages: a command-line tool for automated macromolecular structure visualization
JF  - Bioinformatics
VL  - 39
IS  - 12
SP  - 1-4
EP  - 1-4
PB  - Oxford University Press
SN  - 13674803
KW  - biomacromolecules
KW  - organelle- and cell-sized models
KW  - PDBImages
KW  - open-source
KW  - visualization
KW  - databases
KW  - software
KW  - 3D structure
KW  - bioinformatics
UR  - https://academic.oup.com/bioinformatics/article/39/12/btad744/7470737
N2  - PDBImages is an innovative, open-source Node.js package that harnesses the power of the popular macromolecule structure visualization software Mol*. Designed for use by the scientific community, PDBImages provides a means to generate high-quality images for PDB and AlphaFold DB models. Its unique ability to render and save images directly to files in a browserless mode sets it apart, offering users a streamlined, automated process for macromolecular structure visualization. Here, we detail the implementation of PDBImages, enumerating its diverse image types, and elaborating on its user-friendly setup. This powerful tool opens a new gateway for researchers to visualize, analyse, and share their work, fostering a deeper understanding of bioinformatics.
ER  -

MIDLIK, Adam; Sreenath NAIR; Stephen ANYANGO; Mandar DESHPANDE; David SEHNAL; Mihaly VARADI a Sameer VELANKAR. PDBImages: a command-line tool for automated macromolecular structure visualization. \textit{Bioinformatics}. Oxford: Oxford University Press, 2023, roč.~39, č.~12, s.~1-4. ISSN~1367-4803. Dostupné z: https://doi.org/10.1093/bioinformatics/btad744.

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