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

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.

SUBMITTER: Jariwala S

PROVIDER: S-EPMC5612356 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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

Jariwala Shashank S Skjærven Lars L Yao Xin-Qiu XQ Grant Barry J BJ

Journal of visualized experiments : JoVE 20170716 125

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 e ...[more]

PMID: 28745621

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