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eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces

SUMMARY: Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Br...

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Detalles Bibliográficos
Autores principales: Orellana, Laura, Gustavsson, Johan, Bergh, Cathrine, Yoluk, Ozge, Lindahl, Erik
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748756/
https://www.ncbi.nlm.nih.gov/pubmed/30838394
http://dx.doi.org/10.1093/bioinformatics/btz104
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author Orellana, Laura
Gustavsson, Johan
Bergh, Cathrine
Yoluk, Ozge
Lindahl, Erik
author_facet Orellana, Laura
Gustavsson, Johan
Bergh, Cathrine
Yoluk, Ozge
Lindahl, Erik
author_sort Orellana, Laura
collection PubMed
description SUMMARY: Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships. AVAILABILITY AND IMPLEMENTATION: eBDIMS is available online: http://ebdims.biophysics.se/ or as standalone software: https://github.com/laura-orellana/eBDIMS, https://github.com/cabergh/eBDIMS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-67487562019-09-23 eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces Orellana, Laura Gustavsson, Johan Bergh, Cathrine Yoluk, Ozge Lindahl, Erik Bioinformatics Applications Notes SUMMARY: Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships. AVAILABILITY AND IMPLEMENTATION: eBDIMS is available online: http://ebdims.biophysics.se/ or as standalone software: https://github.com/laura-orellana/eBDIMS, https://github.com/cabergh/eBDIMS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2019-09-15 2019-02-19 /pmc/articles/PMC6748756/ /pubmed/30838394 http://dx.doi.org/10.1093/bioinformatics/btz104 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Orellana, Laura
Gustavsson, Johan
Bergh, Cathrine
Yoluk, Ozge
Lindahl, Erik
eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
title eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
title_full eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
title_fullStr eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
title_full_unstemmed eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
title_short eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
title_sort ebdims server: protein transition pathways with ensemble analysis in 2d-motion spaces
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6748756/
https://www.ncbi.nlm.nih.gov/pubmed/30838394
http://dx.doi.org/10.1093/bioinformatics/btz104
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