Powerful and blazing-fast tool for handling 3D macromolecular data in the browser
CoordinateServer
Streaming of selected parts of 3D molecular data
BinaryCIF
Efficient macromolecular data format
LiteMol

Powerful and blazing-fast tool for handling 3D macromolecular data in the browser

VIEWER

Web based molecular viewer

LiteMol Viewer is an HTML5 web application for 3D visualization of molecules and other related data.

Among other things, LiteMol provides:

  • Standard visualizations: cartoons, surface, balls and sticks, etc.

  • Assemblies and symmetry mates.

  • Electron Density and CryoEM maps.

  • Integration with PDBe API: view and explore validation and annotation data.

  • Integration with the Coordinate Server: download only parts of structures you are interested in.

  • Support for the BinaryCIF format that reduces the amount of data that needs to be sent to the client several times.

More information about LiteMol can be found on the wiki or watch some of our YouTube tutorials.

PLUGIN

Embed LiteMol in your web pages

LiteMol can be embedded in your pages as a plugin to enable rich interaction with your data. For example, PDBe uses LiteMol in simultaneously highlighting the 1D, 2D, and 3D structure of a protein.

To include LiteMol in your applications, you can start by looking at the examples in the GitHub repository. LiteMol is written in TypeScript, a typed extension of JavaScript (but can be consumed from plain old JS as well) and uses WebGL for 3D visualization. For simple use cases, PDB Component Library wrapper can be used.

If you need more help integrating it or are missing some key functionality, please contact us or use the GitHub issues page.

LIBRARY

Parsers and data representation for molecular data

LiteMol can serve as a library that provides parsers and data reprepresentation for molecular data that could be used to build powerful applications.

For example, the CoordinateServer uses LiteMol to load, represent, and query the molecular data.

CoordinateServer

On-demand streaming of selected parts of 3D molecular data

CoordinateServer is a fast, web-based tool for returning a subset of mmCIF coordinate data for a PDB entry held in the PDB archive. The server is able to return the specific portions of the structure that are relevant, as specified in your query. For example, the coordinates of the atoms within a 5-A radius around the ligand binding site, including symmetry mates. As a result, it greatly reduces the time needed to transmit and manipulate the data.

Among other cool features, it supports the BinaryCIF format that further reduces the amount of data that needs to be sent to the browser.

CoordinateServer is also available as a service provided by PDBe.

Stay tuned, it will be open sourced soon.

BinaryCIF

Efficient macromolecular data format

BinaryCIF is a data format that stores the text based CIF using a more efficient binary encoding. BinaryCIF files take up to an order of magnitude less space than the corresponding CIF files.

mmCIF data stored using BinaryCIF correspond exactly to the standard text format defined by wwPDB. As a result, existing software supporting the mmCIF could be very easily modified to support BinaryCIF as well.

A more comprehensive benchmark of BinaryCIF can be found in the BinaryCIF GitHub repository.