Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and struct...

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Detalles Bibliográficos
Autores principales: Jariwala, Shashank, Skjærven, Lars, Yao, Xin-Qiu, Grant, Barry J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MyJove Corporation 2017
Materias:
Biochemistry
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5612356/
https://www.ncbi.nlm.nih.gov/pubmed/28745621
http://dx.doi.org/10.3791/55640
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author Jariwala, Shashank
Skjærven, Lars
Yao, Xin-Qiu
Grant, Barry J.
author_facet Jariwala, Shashank
Skjærven, Lars
Yao, Xin-Qiu
Grant, Barry J.
author_sort Jariwala, Shashank
collection PubMed
description We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis. This integrated functionality provides a complete online workflow for investigating sequence-structure-dynamic relationships within protein families and superfamilies.
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spelling pubmed-56123562017-10-10 Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web Jariwala, Shashank Skjærven, Lars Yao, Xin-Qiu Grant, Barry J. J Vis Exp Biochemistry We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis. This integrated functionality provides a complete online workflow for investigating sequence-structure-dynamic relationships within protein families and superfamilies. MyJove Corporation 2017-07-16 /pmc/articles/PMC5612356/ /pubmed/28745621 http://dx.doi.org/10.3791/55640 Text en Copyright © 2017, Journal of Visualized Experiments http://creativecommons.org/licenses/by-nc-nd/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visithttp://creativecommons.org/licenses/by-nc-nd/3.0/
spellingShingle Biochemistry
Jariwala, Shashank
Skjærven, Lars
Yao, Xin-Qiu
Grant, Barry J.
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
title Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
title_full Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
title_fullStr Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
title_full_unstemmed Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
title_short Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
title_sort investigating protein sequence-structure-dynamics relationships with bio3d-web
topic Biochemistry
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5612356/
https://www.ncbi.nlm.nih.gov/pubmed/28745621
http://dx.doi.org/10.3791/55640
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