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The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations

We present the Biological Structure Model Archive (BSM-Arc, https://bsma.pdbj.org), which aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce a specifi...

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Detalles Bibliográficos
Autores principales: Bekker, Gert-Jan, Kawabata, Takeshi, Kurisu, Genji
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Berlin Heidelberg 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242595/
https://www.ncbi.nlm.nih.gov/pubmed/32026396
http://dx.doi.org/10.1007/s12551-020-00632-5
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author Bekker, Gert-Jan
Kawabata, Takeshi
Kurisu, Genji
author_facet Bekker, Gert-Jan
Kawabata, Takeshi
Kurisu, Genji
author_sort Bekker, Gert-Jan
collection PubMed
description We present the Biological Structure Model Archive (BSM-Arc, https://bsma.pdbj.org), which aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce a specific data format for the raw data, depositors are free to upload their data without any prior conversion. Besides uploading raw data, BSM-Arc enables depositors to annotate their data with additional explanations and figures. Furthermore, via our WebGL-based molecular viewer Molmil, it is possible to recreate 3D scenes as shown in the corresponding scientific article in an interactive manner. To submit a new entry, depositors require an ORCID ID to login, and to finally publish the data, an accompanying peer-reviewed paper describing the work must be associated with the entry. Submitting their data enables researchers to not only have an external backup but also provide an opportunity to promote their work via an interactive platform and to provide third-party researchers access to their raw data.
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spelling pubmed-72425952020-06-03 The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations Bekker, Gert-Jan Kawabata, Takeshi Kurisu, Genji Biophys Rev Review We present the Biological Structure Model Archive (BSM-Arc, https://bsma.pdbj.org), which aims to collect raw data obtained via in silico methods related to structural biology, such as computationally modeled 3D structures and molecular dynamics trajectories. Since BSM-Arc does not enforce a specific data format for the raw data, depositors are free to upload their data without any prior conversion. Besides uploading raw data, BSM-Arc enables depositors to annotate their data with additional explanations and figures. Furthermore, via our WebGL-based molecular viewer Molmil, it is possible to recreate 3D scenes as shown in the corresponding scientific article in an interactive manner. To submit a new entry, depositors require an ORCID ID to login, and to finally publish the data, an accompanying peer-reviewed paper describing the work must be associated with the entry. Submitting their data enables researchers to not only have an external backup but also provide an opportunity to promote their work via an interactive platform and to provide third-party researchers access to their raw data. Springer Berlin Heidelberg 2020-02-05 /pmc/articles/PMC7242595/ /pubmed/32026396 http://dx.doi.org/10.1007/s12551-020-00632-5 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Review
Bekker, Gert-Jan
Kawabata, Takeshi
Kurisu, Genji
The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
title The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
title_full The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
title_fullStr The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
title_full_unstemmed The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
title_short The Biological Structure Model Archive (BSM-Arc): an archive for in silico models and simulations
title_sort biological structure model archive (bsm-arc): an archive for in silico models and simulations
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7242595/
https://www.ncbi.nlm.nih.gov/pubmed/32026396
http://dx.doi.org/10.1007/s12551-020-00632-5
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