title: A real-time all-atom structural search engine for proteins.
abstract: Protein designers use a wide variety of software tools for de novo 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 http://www.degradolab.org/suns/ and the source code is hosted at https://github.com/godotgildor/Suns (PyMOL plugin, BSD license), https://github.com/Gabriel439/suns-cmd (command line client, BSD license), and https://github.com/Gabriel439/suns-search (search engine server, GPLv2 license).
authors: Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America.
authors: Gabriel
authors: G
authors: Gonzalez
authors: Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America.
authors: Brett
authors: B
authors: Hannigan
authors: Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America.
authors: William F
authors: WF
authors: DeGrado
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D030562:Databases, Protein; D020407:Internet; D015202:Protein Engineering; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D057386:Search Engine / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins