Section outline

  • Several resources are providing easy access to protein structure information simply from a web interface. In this chapter, we will explore several commonly used web sites for exploring protein structures from a web browser.

    The structure view of the PDB allows to experience various viewers. Please check them out!

    The defacto standard JMOL

    JMOL/JSMOL is the most common used web interface to molecular structure. <a href="https://www.stolaf.edu/people/hansonr/">Bob Hanson at St. Olaf</a> is the main developer. JMOL has a large community and many features, which makes it loved by chemists and structural biologists.

    The Newcomers:

    PV

    PV is implemented in javascript rather than java, thereby alleviating the trouble connected with java plugins and ever-changing browser security settings. PV is fast and offers a pleasant style along with a powerful API to interface with it.

    NGL

    NGL is developed by Axel Rose and actively supported by the RCSB PDB. It features a very fast rendering and builds upon the new mmtf format for 3D structure information.

    Proprietary:

    MOLSOFT LLC develops ICMBrowser, which is available in a free version, some features require unlocking.

    BioNext develops more than just a viewer, but it features great graphics! It is not free, though!

    Others

    Java based alternatives are Aquaria, OpenAstexViewer, both are not widely used, but Aquria has nice integrated data visualisation beyond structure and OpenAstexViewer appealing graphical defaults and powerful selections.