Cargando…

Stmol: A component for building interactive molecular visualizations within streamlit web-applications

Streamlit is an open-source Python coding framework for building web-applications or “web-apps” and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizati...

Descripción completa

Detalles Bibliográficos
Autores principales: Nápoles-Duarte, J.M., Biswas, Avratanu, Parker, Mitchell I., Palomares-Baez, J.P., Chávez-Rojo, M. A., Rodríguez-Valdez, L. M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9538479/
https://www.ncbi.nlm.nih.gov/pubmed/36213112
http://dx.doi.org/10.3389/fmolb.2022.990846
_version_ 1784803354854031360
author Nápoles-Duarte, J.M.
Biswas, Avratanu
Parker, Mitchell I.
Palomares-Baez, J.P.
Chávez-Rojo, M. A.
Rodríguez-Valdez, L. M.
author_facet Nápoles-Duarte, J.M.
Biswas, Avratanu
Parker, Mitchell I.
Palomares-Baez, J.P.
Chávez-Rojo, M. A.
Rodríguez-Valdez, L. M.
author_sort Nápoles-Duarte, J.M.
collection PubMed
description Streamlit is an open-source Python coding framework for building web-applications or “web-apps” and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps. Stmol can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck. On the user-end, Stmol does not require expertise to interactively navigate. On the developer-end, Stmol can be easily integrated within structural bioinformatic and cheminformatic pipelines to provide a simple means for user-end researchers to advance biological studies and drug discovery efforts. In this paper, we highlight a few examples of how Stmol has already been utilized by scientific communities to share interactive molecular visualizations of protein and ligand structures from known open databases. We hope Stmol will be used by researchers to build additional open-sourced web-apps to benefit current and future generations of scientists.
format Online
Article
Text
id pubmed-9538479
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-95384792022-10-08 Stmol: A component for building interactive molecular visualizations within streamlit web-applications Nápoles-Duarte, J.M. Biswas, Avratanu Parker, Mitchell I. Palomares-Baez, J.P. Chávez-Rojo, M. A. Rodríguez-Valdez, L. M. Front Mol Biosci Molecular Biosciences Streamlit is an open-source Python coding framework for building web-applications or “web-apps” and is now being used by researchers to share large data sets from published studies and other resources. Here we present Stmol, an easy-to-use component for rendering interactive 3D molecular visualizations of protein and ligand structures within Streamlit web-apps. Stmol can render protein and ligand structures with just a few lines of Python code by utilizing popular visualization libraries, currently Py3DMol and Speck. On the user-end, Stmol does not require expertise to interactively navigate. On the developer-end, Stmol can be easily integrated within structural bioinformatic and cheminformatic pipelines to provide a simple means for user-end researchers to advance biological studies and drug discovery efforts. In this paper, we highlight a few examples of how Stmol has already been utilized by scientific communities to share interactive molecular visualizations of protein and ligand structures from known open databases. We hope Stmol will be used by researchers to build additional open-sourced web-apps to benefit current and future generations of scientists. Frontiers Media S.A. 2022-09-23 /pmc/articles/PMC9538479/ /pubmed/36213112 http://dx.doi.org/10.3389/fmolb.2022.990846 Text en Copyright © 2022 Nápoles-Duarte, Biswas, Parker, Palomares-Baez, Chávez-Rojo and Rodríguez-Valdez. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Nápoles-Duarte, J.M.
Biswas, Avratanu
Parker, Mitchell I.
Palomares-Baez, J.P.
Chávez-Rojo, M. A.
Rodríguez-Valdez, L. M.
Stmol: A component for building interactive molecular visualizations within streamlit web-applications
title Stmol: A component for building interactive molecular visualizations within streamlit web-applications
title_full Stmol: A component for building interactive molecular visualizations within streamlit web-applications
title_fullStr Stmol: A component for building interactive molecular visualizations within streamlit web-applications
title_full_unstemmed Stmol: A component for building interactive molecular visualizations within streamlit web-applications
title_short Stmol: A component for building interactive molecular visualizations within streamlit web-applications
title_sort stmol: a component for building interactive molecular visualizations within streamlit web-applications
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9538479/
https://www.ncbi.nlm.nih.gov/pubmed/36213112
http://dx.doi.org/10.3389/fmolb.2022.990846
work_keys_str_mv AT napolesduartejm stmolacomponentforbuildinginteractivemolecularvisualizationswithinstreamlitwebapplications
AT biswasavratanu stmolacomponentforbuildinginteractivemolecularvisualizationswithinstreamlitwebapplications
AT parkermitchelli stmolacomponentforbuildinginteractivemolecularvisualizationswithinstreamlitwebapplications
AT palomaresbaezjp stmolacomponentforbuildinginteractivemolecularvisualizationswithinstreamlitwebapplications
AT chavezrojoma stmolacomponentforbuildinginteractivemolecularvisualizationswithinstreamlitwebapplications
AT rodriguezvaldezlm stmolacomponentforbuildinginteractivemolecularvisualizationswithinstreamlitwebapplications