Abstract
Summary: 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
Highlights
Many structures are available for homologous proteins determined under different crystallization conditions and oligomerization states
To this end we have developed Bio3D-web—a web application that implements a complete workflow for user customized investigation of protein sequence-structure-dynamic relationships
Bio3D-web is an online application for analyzing user defined heterogeneous biomolecular structure data
Summary
Many structures are available for homologous proteins determined under different crystallization conditions and oligomerization states. The NMA here is performed on all selected structures in a way that facilitates the interpretation of their structural similarity and dissimilarity trends (Yao et al, 2016) This allows a user to explore dynamic trends in all crystalized states in relation to each other without the conventional caveat of potentially over-interpreting the differences between extreme cases or a single artifactual structure. These results indicate the existence of three major Rho superfamily conformational states that differ by a collective displacement of two nucleotide-binding site regions, which in turn display significantly distinct flexibilities upon nucleotide binding. Further example application of Bio3D-web to a range of distinct protein families is presented as interactive demos online (http://thegrantlab.org/bio3d-web)
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