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Updated: Dec 29, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Comparative Protein Structure Analysis with Bio3D-Web
Barry J Grant1, Lars Skjærven2, Xin-Qiu Yao3
1Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA. bjgrant@ucsd.edu.
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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