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J Vis Exp. 2017 Jul 16;(125). doi: 10.3791/55640.

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

Author information

1
Department of Computational Medicine and Bioinformatics, University of Michigan Medical School.
2
Department of Biomedicine, University of Bergen.
3
Department of Computational Medicine and Bioinformatics, University of Michigan Medical School; bjgrant@umich.edu.

Abstract

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.

PMID:
28745621
PMCID:
PMC5612356
DOI:
10.3791/55640
[Indexed for MEDLINE]
Free PMC Article

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