pdb3D is a package to visualize the 3D strucutre of proteins from Protein Data base or users’ own pdb file. pdb3D annotes the important structures from database such as Pfam and calculate similarity between two pdb files.
To install the released version of pdb3D from GitHub with:
require("devtools")
devtools::install_github("kevin949373048/pdb3D", build_vignettes = TRUE)
library("pdb3D")To run the ShinyApp:
runPdb3D()an overview of pdb3D is illustated below:
pdb3D contains 6 functions.
For carrying out protein structure visualization: show3Dmol, changeStyle.
parseSpec is the helper function for colorPfam to have proper input
Pfam structure annotation: colorPfam.
testSimilarity will compare the sequence similarity of two pdb files. The function use RecordLinkage::levenshteinSim() to compute the similarity between two sequences.
compareTwoPDB will compare the structure similarity of two pdb files.
To list all functions available in the package:
ls("package:pdb3D")
changeStyle("stick", "1a2b", "red")
Figure 1, show the
change changeStyle function
show3Dmol("1a2b")
Figure 2, show the
show3Dmol function display protein structure.
colorPfam("1a2b")
Figure 3, show the
Pfam families highlighted in blue in the protein structure.
Below is the shiny app version of the package. Tutorial is in Vignettes.
The package tree structure is provided below: 
## Tutorials For tutorials, refer to
the vignette:
browseVignettes("pdb3D")
Wenkai Cao ([email protected]).
All functions are original idea from Wenkai Cao. The functions use packages from CRAN to better development. show3Dmol, changeStyle, colorPfam and compareTwoPDB are heabily depend on 3dmol.js for visualization. colorPfam depends on bio3D package for pfam data input. show3Dmol use r3dmol for in app visualization, changeStyle, colorPfam and compareTwoPDB depend on shiny and need to close the shiny app window for additional visualization.
pdb3D welcomes issues, enhancement requests, and other contributions. To submit an issue, use the GitHub issues.
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Nicholas Rego and David Koes 3Dmol.js: molecular visualization with WebGL Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829.
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Winston Chang, Joe Cheng, JJ Allaire, Yihui Xie and Jonathan McPherson (2020). shiny: Web Application Framework for R. R package version 1.5.0. https://CRAN.R-project.org/package=shiny.
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Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
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S. El-Gebali, J. Mistry, A. Bateman, S.R. Eddy, A. Luciani, S.C. Potter, M. Qureshi, L.J. Richardson, G.A. Salazar, A. Smart, E.L.L. Sonnhammer, L. Hirsh, L. Paladin, D. Piovesan, S.C.E. Tosatto, R.D. Finn The Pfam protein families database in 2019 Nucleic Acids Research (2019) doi: 10.1093/nar/gky995
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Wei Su (2020). r3dmol: Create Interactive 3D Visualizations of Molecular Data. R package version 0.1.0. https://github.com/swsoyee/r3dmol
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Murat Sariyar and Andreas Borg (2020). RecordLinkage: Record Linkage Functions for Linking and Deduplicating Data Sets. R package version 0.4-12.1. https://CRAN.R-project.org/package=RecordLinkage
This package was developed as part of an assessment for 2020 BCB410H: Applied Bioinfor-matics, University of Toronto, Toronto, CA