What is dms-viz? ​

Hi there 👋, if you have mutation-based data you want to view on an interactive 3D protein structure, you're in the right place! dms-viz is a tool that helps you take quantitative data associated with mutations to a protein and analyze that data with intuitive visual summaries and an interactive 3D protein structure. Visualizations created with dms-viz are flexible, customizable, and shareable.

Purpose ​

Many biological questions require a thorough understanding of how mutations to a protein impact its functions. High-throughput techniques such as deep-mutational scanning (DMS) have greatly expanded the number of mutation-function datasets. For instance, DMS has been used to determine how mutations to viral proteins affect antibody escape, receptor affinity, and essential functions such as viral genome transcription and replication.

The mutation-based data generated by these approaches is often best understood in the context of a protein’s 3D structure; for instance, to assess questions like how mutations that affect antibody escape relate to the physical antibody binding epitope on the protein. However, current approaches for visualizing mutation data in the context of a protein’s structure are often cumbersome and require multiple steps and software. To streamline the visualization of mutation-associated data in the context of a protein structure, we developed a web-based tool, dms-viz. With dms-viz, users can straightforwardly visualize mutation-based data such as those from DMS experiments in the context of a 3D protein model in an interactive format.

Why use dms-viz? ​

• Flexible Inputs

  Our command-line tool, configure-dms-viz, helps streamline data formatting by facilitating the integration of data from different sources into a singular, universal JSON specification file. Moreover, configure-dms-viz helps you define custom filters and tooltips, and identify common errors.

• Customizable Visualizations

  We've designed dms-viz with customization in mind. You can tailor the appearance of the protein structure to fit your needs. Furthermore, you can extend the functionality of the tool with custom filters, tooltips, colors, and more.

• Shareable URLs

  If your data is hosted online (e.g. in a GitHub repository), you can share your data with URLs that automatically load the visualization while keeping your settings. However, if you don't want to host your data online, you can still use dms-viz with locally stored .json files.

Contributing to dms-viz ​

dms-viz has two components:

1. A command line interface (CLI) for formatting data that was written in Python using the click API.
2. A web-based visualization tool written in Javascript using primarily the libraries D3.js for making the visualizations and NGL.js for creating interactive molecular structures.

If you're interested in contributing, check out the Contributing Guide for details.

Citation ​

If you end up using dms-viz in your paper, please cite us!

Citation pending...

Citation pending...