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Comparative Protein Structure Analysis with Bio3D-Web

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Structural Bioinformatics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2112))

Abstract

Bio3D-web is an online application for the interactive analysis of sequence-structure-dynamics relationships in user-defined protein structure sets. Major functionality includes structure database searching, sequence and structure conservation assessment, inter-conformer relationship mapping and clustering with principal component analysis (PCA), and flexibility prediction and comparison with ensemble normal mode analysis (eNMA). Collectively these methods allow users to start with a single sequence or structure and characterize the structural, conformational, and internal dynamic properties of homologous proteins for which there are high-resolution structures available. Functionality is also provided for the generation of custom PDF, Word, and HTML analysis reports detailing all user-specified analysis settings and corresponding results. Bio3D-web is available at http://thegrantlab.org/bio3d/webapps, as a Docker image https://hub.docker.com/r/bio3d/bio3d-web/, or downloadable source code https://bitbucket.org/Grantlab/bio3d-web.

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References

  1. Skjaerven L, Jariwala S, Yao XQ, Grant BJ (2016) Online interactive analysis of protein structure ensembles with Bio3D-web. Bioinformatics 32(22):3510–3512. https://doi.org/10.1093/bioinformatics/btw482. Epub 2016/07/18. PubMed PMID: 27423893; PMCID: PMC5181562

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Acknowledgments

We thank Shashank Jariwala, Hongyang Li, and Dr. Guido Scarabelli for extensive testing throughout development as well as the Bio3D user community for their feedback and comments that have improved this application.

Author information

Authors and Affiliations

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

    Barry J. Grant

  2. Department of Biomedicine, University of Bergen, Bergen, Norway

    Lars Skjærven

  3. Department of Chemistry, Georgia State University, Atlanta, GA, USA

    Xin-Qiu Yao

Authors
  1. Barry J. Grant
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  2. Lars Skjærven
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  3. Xin-Qiu Yao
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Corresponding author

Correspondence to Barry J. Grant .

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Editors and Affiliations

  1. Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary

    Zoltán Gáspári

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© 2020 Springer Science+Business Media, LLC, part of Springer Nature

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Grant, B.J., Skjærven, L., Yao, XQ. (2020). Comparative Protein Structure Analysis with Bio3D-Web. In: Gáspári, Z. (eds) Structural Bioinformatics. Methods in Molecular Biology, vol 2112. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0270-6_2

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  • DOI: https://doi.org/10.1007/978-1-0716-0270-6_2

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0269-0

  • Online ISBN: 978-1-0716-0270-6

  • eBook Packages: Springer Protocols

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