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R Shiny wrapper for Mol* (/’molstar/) - A visualization toolkit of large-scale molecular data

Based on Mol* (/’molstar/) and powered by shiny.react

We created a R Shiny wrapper based on shiny.react and molstar-react (node.js library) that gives all the powerful tools of Mol* open-source toolkit for visualization and analysis of large-scale molecular data.

This package exports three new components that can be used in a Shiny application.

  • Molstar creates a Molstar visualization of a protein using an URL to a valid filetype supported by Molstar or a “Protein Data Bank” id (pdbId). See more below for available databases to find a valid pdbId.
  • AlphaFoldMolstar similar to the Molstar component, but uses the UniProt id in the AlphaFold database to display the protein.
  • AlphaFoldDetails creates a component that retrieves details of an AlphaFold protein id (title, download links and a Predict Aligned Error image)

How to find a valid id or url?

A valid pdbId can be found in public databases such as:

The uniProtId can be found in any of the AlphaFold databases:

Getting started

To install the package, run:


Take a look at basic example app to start working with shiny.molstar.

To learn about the Mol* language, follow the Viewer documentation.


A good way to learn more is to look at the examples. Once you install the library, you can run them with shiny.molstar::runExample function.


Full page example

Creating a full page viewer on a sample molecule (example also available at inst/examples/FullPage.R)


  ui = tagList(
    tags$style(HTML("html, body { margin: 0; }")),
      pdbId = "1LOL",
      useInterface = TRUE,
      showControls = TRUE,
      showAxis = TRUE
  server = function(input, output) {

Full page example

Using AlphaFold database and details

Running an example from the package (located at inst/examples/AlphaFoldDetails.R).

You can click on the button on the bottom of the example to get the minimal code to reproduce the same Shiny application (unstyled and without the footer).


AlphaFold with details


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