Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F24%3A00139730" target="_blank" >RIV/00216224:14310/24:00139730 - isvavai.cz</a>

Výsledek na webu

<a href="https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.1099" target="_blank" >https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.1099</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/cpz1.1099" target="_blank" >10.1002/cpz1.1099</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit

Popis výsledku v původním jazyce

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

Název v anglickém jazyce

Describing and Sharing Molecular Visualizations Using the MolViewSpec Toolkit

Popis výsledku anglicky

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

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

<a href="/cs/project/GM22-30571M" target="_blank" >GM22-30571M: Cell*: webová platforma pro vizualizaci, modelování a dynamiku organelových a buněčných struktur</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2024

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Current Protocols

ISSN

2691-1299

e-ISSN

2691-1299

Svazek periodika

4

Číslo periodika v rámci svazku

7

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

23

Strana od-do

1-23

Kód UT WoS článku

001270762400001

EID výsledku v databázi Scopus

2-s2.0-85198756612