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. 2016 Nov 15;32(22):3510-3512.
doi: 10.1093/bioinformatics/btw482. Epub 2016 Jul 16.

Online Interactive Analysis of Protein Structure Ensembles With Bio3D-web

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Free PMC article

Online Interactive Analysis of Protein Structure Ensembles With Bio3D-web

Lars Skjærven et al. Bioinformatics. .
Free PMC article

Abstract

Bio3D-web is an online application for analyzing the sequence, structure and conformational heterogeneity of protein families. Major functionality is provided for identifying protein structure sets for analysis, their alignment and refined structure superposition, sequence and structure conservation analysis, mapping and clustering of conformations and the quantitative comparison of their predicted structural dynamics.

Availability: Bio3D-web is based on the Bio3D and Shiny R packages. All major browsers are supported and full source code is available under a GPL2 license from http://thegrantlab.org/bio3d-web CONTACT: bjgrant@umich.edu or lars.skjarven@uib.no.

Figures

Fig. 1.
Fig. 1.
Bio3D-web analysis of Rho GTPases. (A) Visualization of the first principal component (PC) characterizing the major conformational variations. (B) Structures projected onto their two first PCs. Each point (or structure) is colored according to user specified criteria, in this case PCA-based clustering results. (C) Contribution of each residue to the first PC. (D) Ensemble normal mode analysis reveals the enhanced local dynamics of nucleotide free states (red) relative to the GTP- and GDP-bound (green and black) structures. Positions with significantly distinct flexibilities between states are indicated with light blue rectangles (P < 0.05) (Color version of this figure is available at Bioinformatics online.)

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