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
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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.
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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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