README.md

In JerrieFeng/pdbSelectOcclude: Select occluding structures in a 3D molecular visualization environment

pdbSelectOcclude

Description

pdbSelectOcclude is an R package for visualizing relationships between protein structural and non-spatial data, and for selecting occluding structures in a 3D molecular visualization environment. The objective of the package is to help improve current selecting (aka brushing) protein structural residues techniques. Currently, most brushing techniques (such as point-and-click) for 3D spatial data do not work well for occluded structures (i.e. molecular structures that are not visible from the surface). The package is targeted for those who are interested in molecular visualization.

This includes the main components: DESCRIPTION, NAMESPACE, man subdirectory and R subdirectory. Additionally, licence, README and subdirectories vignettes, tests, data and inst are also explored. To develop this package, R (version 4.0.2) and Mac platform was used.

Installation

You can install the development version of pdbSelectOcclude like so:

require("devtools")
devtools::install_github("JerrieFeng/pdbSelectOcclude", build_vignettes = TRUE)
library("pdbSelectOcclude")

To run the Shiny App:

#Example of visualizing a protein
runModel(pdb2, "1SI4")

#Example for running individual selecting components:
# 1. Selecting by AA
selAASlider(pdb, "1bm8")
# 2. Selecting by Chains
selChainSlider(pdb2, "1SI4")
# 3. Selecting by polarity
selHphobSlider(pdb, "1bm8")
# 4. Selecting by UniProt values
selUniShiny(pdb, "1bm8")

Overview

ls("package:pdbSelectOcclude")
data(package = "pdbSelectOcclude") # includes PDB files

pdbSelectOcclude contains 6 functions. The showInfoPDB function takes a PDB file as input, and then returns the AA (amino acid) and chain information of the chosen protein. selAA function allow users to select an [occluded] AA to view and interact with. selChain function allow users to select an [occluded] chain to view and interact with. selHphob function allow users to interact with the hydrophobicity/polarity of the AA components through Shiny App. selUniProt allows users to select and interact according to the UniProt values by Shiny App.

An overview of the package and examples of what it should produce is illustrated below.

browseVignettes("pdbSelectOcclude")

Contributions

The author of the package is Jerrie Feng. All the functions rely on bio3d package to read and extract information from the PDB files. selAA and selChain makes use of r3dmol and dplyr to visualize the protein as a 3D molecule. selAASlider and selChainSlider make use of Shiny to create the slider and allow users to interact with the proteins.

References

Chang, W, et al. (2017). Using sliders. Shiny from Rstudio. https://shiny.rstudio.com/articles/sliders.html.

Chang, W, et al. (2021). shiny: Web Application Framework for R. R package version 1.7.1. https://CRAN.R-project.org/package=shiny.

Skjaerven, L., Yao X.Q., Grant B.J. (2006). Getting started with Bio3D. Grant Lab: ComputationalBiophysics & Bioinformatics. http://thegrantlab.org/bio3d/articles/online/intro_vignette/Bio3D_introduction.html#references-1.

Skjaerven, L., Yao X.Q., Grant B.J. (2020). chain.pdb: Find Possible PDB Chain Breaks. bio3D. https://rdrr.io/cran/bio3d/man/chain.pdb.html.

Su, W., Johnston, B. (2021). r3dmol: Create Interactive 3D Visualizations of Molecular Data. Github.https://github.com/swsoyee/r3dmol.

Su, W., Johnston, B. (2021). r3dmol-shiny: Shiny bindings for r3dmol. https://rdrr.io/cran/r3dmol/man/r3dmol-shiny.html.

Acknowledgements

This package was developed as part of an assessment for 2021 BCB410H: Applied Bioinfor-matics, University of Toronto, Toronto, CANADA.

JerrieFeng/pdbSelectOcclude documentation built on May 12, 2022, 8:07 a.m.