Describing and Sharing Molecular Visualizations Using the
MolViewSpec Toolkit

J 2024

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit

BITTRICH, Sebastian; Adam MIDLIK; Mihaly VARADI; Sameer VELANKAR; Stephen K BURLEY et al.

Základní údaje

Originální název

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit

Autoři

BITTRICH, Sebastian; Adam MIDLIK; Mihaly VARADI; Sameer VELANKAR; Stephen K BURLEY; Jasmine Y YOUNG; David SEHNAL a Brinda VALLAT

Vydání

Current Protocols, Wiley, 2024, 2691-1299

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 2.200

Označené pro přenos do RIV

Ano

Kód RIV

RIV/00216224:14310/24:00139730

Organizační jednotka

Přírodovědecká fakulta

Klíčová slova anglicky

3D visualization; interoperability; macromolecular structure; mmCIF; Protein Data Bank

Štítky

143160, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 31. 1. 2025 17:08, Mgr. Marie Novosadová Šípková, DiS.

Anotace

V originále

With the ever-expanding toolkit of molecular viewers, the ability to visualize macromolecular structures has never been more accessible. Yet, the idiosyncratic technical intricacies across tools and the integration complexities associated with handling structure annotation data present significant barriers to seamless interoperability and steep learning curves for many users. The necessity for reproducible data visualizations is at the forefront of the current challenges. Recently, we introduced MolViewSpec (homepage: , GitHub project: ), a specification approach that defines molecular visualizations, decoupling them from the varying implementation details of different molecular viewers. Through the protocols presented herein, we demonstrate how to use MolViewSpec and its 3D view-building Python library for creating sophisticated, customized 3D views covering all standard molecular visualizations. MolViewSpec supports representations like cartoon and ball-and-stick with coloring, labeling, and applying complex transformations such as superposition to any macromolecular structure file in mmCIF, BinaryCIF, and PDB formats. These examples showcase progress towards reusability and interoperability of molecular 3D visualization in an era when handling molecular structures at scale is a timely and pressing matter in structural bioinformatics as well as research and education across the life sciences. (c) 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Creating a MolViewSpec view using the MolViewSpec Python packageBasic Protocol 2: Creating a MolViewSpec view with reference to MolViewSpec annotation filesBasic Protocol 3: Creating a MolViewSpec view with labels and other advanced featuresSupport Protocol 1: Computing rotation and translation vectorsSupport Protocol 2: Creating a MolViewSpec annotation file

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

BITTRICH, Sebastian; Adam MIDLIK; Mihaly VARADI; Sameer VELANKAR; Stephen K BURLEY; Jasmine Y YOUNG; David SEHNAL a Brinda VALLAT. Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit. Current Protocols. Wiley, 2024, roč. 4, č. 7, s. 1-23. ISSN 2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.1099.

@article{2473040,
   author = {Bittrich, Sebastian and Midlik, Adam and Varadi, Mihaly and Velankar, Sameer and Burley, Stephen K and Young, Jasmine Y and Sehnal, David and Vallat, Brinda},
   article_number = {7},
   doi = {https://doi.org/10.1002/cpz1.1099},
   keywords = {3D visualization; interoperability; macromolecular structure; mmCIF; Protein Data Bank},
   language = {eng},
   issn = {2691-1299},
   journal = {Current Protocols},
   title = {Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit},
   url = {https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.1099},
   volume = {4},
   year = {2024}
}

TY  - JOUR
ID  - 2473040
AU  - Bittrich, Sebastian - Midlik, Adam - Varadi, Mihaly - Velankar, Sameer - Burley, Stephen K - Young, Jasmine Y - Sehnal, David - Vallat, Brinda
PY  - 2024
TI  - Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit
JF  - Current Protocols
VL  - 4
IS  - 7
SP  - 1-23
EP  - 1-23
PB  - Wiley
SN  - 26911299
KW  - 3D visualization
KW  - interoperability
KW  - macromolecular structure
KW  - mmCIF
KW  - Protein Data Bank
UR  - https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.1099
N2  - With the ever-expanding toolkit of molecular viewers, the ability to visualize macromolecular structures has never been more accessible. Yet, the idiosyncratic technical intricacies across tools and the integration complexities associated with handling structure annotation data present significant barriers to seamless interoperability and steep learning curves for many users. The necessity for reproducible data visualizations is at the forefront of the current challenges. Recently, we introduced MolViewSpec (homepage: , GitHub project: ), a specification approach that defines molecular visualizations, decoupling them from the varying implementation details of different molecular viewers. Through the protocols presented herein, we demonstrate how to use MolViewSpec and its 3D view-building Python library for creating sophisticated, customized 3D views covering all standard molecular visualizations. MolViewSpec supports representations like cartoon and ball-and-stick with coloring, labeling, and applying complex transformations such as superposition to any macromolecular structure file in mmCIF, BinaryCIF, and PDB formats. These examples showcase progress towards reusability and interoperability of molecular 3D visualization in an era when handling molecular structures at scale is a timely and pressing matter in structural bioinformatics as well as research and education across the life sciences. (c) 2024 The Authors. Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Creating a MolViewSpec view using the MolViewSpec Python packageBasic Protocol 2: Creating a MolViewSpec view with reference to MolViewSpec annotation filesBasic Protocol 3: Creating a MolViewSpec view with labels and other advanced featuresSupport Protocol 1: Computing rotation and translation vectorsSupport Protocol 2: Creating a MolViewSpec annotation file
ER  -

BITTRICH, Sebastian; Adam MIDLIK; Mihaly VARADI; Sameer VELANKAR; Stephen K BURLEY; Jasmine Y YOUNG; David SEHNAL a Brinda VALLAT. Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit. \textit{Current Protocols}. Wiley, 2024, roč.~4, č.~7, s.~1-23. ISSN~2691-1299. Dostupné z: https://doi.org/10.1002/cpz1.1099.

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