<div><p>Protein designers use a wide variety of software tools for <i>de novo</i> design, yet their repertoire still lacks a fast and interactive all-atom search engine. To solve this, we have built the Suns program: a real-time, atomic search engine integrated into the PyMOL molecular visualization system. Users build atomic-level structural search queries within PyMOL and receive a stream of search results aligned to their query within a few seconds. This instant feedback cycle enables a new “designability”-inspired approach to protein design where the designer searches for and interactively incorporates native-like fragments from proven protein structures. We demonstrate the use of Suns to interactively build protein motifs, tertiary interactions, and to identify scaffolds compatible with hot-spot residues. The official web site and installer are located at <a href="http://www.degradolab.org/suns/" target="_blank">http://www.degradolab.org/suns/</a> and the source code is hosted at <a href="https://github.com/godotgildor/Suns" target="_blank">https://github.com/godotgildor/Suns</a> (PyMOL plugin, BSD license), <a href="https://github.com/Gabriel439/suns-cmd" target="_blank">https://github.com/Gabriel439/suns-cmd</a> (command line client, BSD license), and <a href="https://github.com/Gabriel439/suns-search" target="_blank">https://github.com/Gabriel439/suns-search</a> (search engine server, GPLv2 license).</p></div
