NGLVieweR - Visualize and interact with Protein Data Bank (PDB) and structural files in R and Shiny

Click here to view a Shiny application integrating most features of NGLVieweR.

Description

NGLvieweR provides an R interface to the NGL.js JavaScript library. It can be used to visualize and interact with protein data bank (PDB) and structural files in R and Shiny applications. It includes a set of API functions to manipulate the viewer after creation and makes it possible to retrieve data from the visualization into R.

Installation

NGLVieweR is available through GitHub

install.packages("remotes")
remotes::install_github("nvelden/NGLVieweR")

Basics

You can load a PDB (or any other supported structural file) directly or use a PDB code of a structure on RCSB.org. The below minimal example loads the PDB file and displays the structure in a “cartoon” representation.

#Load local pdb file
NGLVieweR("C:/7CID.pdb") %>%
addRepresentation("cartoon")

#Load protein by PDB code
NGLVieweR("7CID") %>%
addRepresentation("cartoon")

Functionality

There are functions provided to:

• Overlay different representation styles
• Alter the stage parameters (e.g. background, zoom- and rotation speed)
• Zoom to specific selections
• Add labels
• Add contacts between residues
• Auto rotate/rock

In Shiny apps, you can manipulate the NGLVieweR widget after creation using specific “API”” calls. Users can for instance add/remove representations, make snapshots, add labels or highlight specific regions. See the Get started section for a complete overview.