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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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The Bio3D packages for structural bioinformatics.

Barry J Grant1, Lars Skjaerven1, Xin-Qiu Yao2

  • 1Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, California, USA.

Protein Science : a Publication of the Protein Society
|August 1, 2020
PubMed
Summary
This summary is machine-generated.

Bio3D R packages offer tools for biomolecular sequence, structure, and dynamics analysis. A new ensemble difference distance matrix analysis (eDDM) method identifies functional determinants in protein structures.

Keywords:
allosteric regulationdistance matrix analysisfunctional dynamicsmolecular dynamicsnormal mode analysisprincipal component analysisprotein sequenceprotein structureprotein structure networkstructural bioinformatics

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Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Bioinformatics software

Background:

  • The Bio3D R package suite provides comprehensive tools for analyzing biomolecular data.
  • Existing functionalities cover sequence and structure analysis, database searching, and network analysis.

Purpose of the Study:

  • To review recent developments in the Bio3D R packages.
  • To introduce a novel method for structural analysis: ensemble difference distance matrix analysis (eDDD).
  • To detail the workflow and application of the eDDM method for identifying functional determinants.

Main Methods:

  • Development and integration of new R packages within the Bio3D family.
  • Implementation of the ensemble difference distance matrix analysis (eDDM) workflow.
  • Application of eDDM to analyze atomic distance matrices across homologous structures.

Main Results:

  • Bio3D packages are now segregated for distinct analyses, enhancing modularity.
  • The eDDM method effectively identifies residue-wise determinants of specific functional processes.
  • The new Bio3D-eddm package supports diverse structure types and integrates with existing Bio3D tools.

Conclusions:

  • The Bio3D suite, including the new eDDM functionality, offers a powerful, automated, and reproducible platform for biomolecular structure-function relationship studies.
  • The eDDM approach facilitates the dissection of complex functional mechanisms from structural data.
  • Bio3D R packages are open-source and readily available for the scientific community.