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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...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2019
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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. |
format | Online Article Text |
id | pubmed-6748756 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
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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