Bubble

Download

User interface

World Wide Web

License

Biology

Computer graphics (images)

Operating system

Set (abstract data type)

Biochemistry

Computer science

Coiled coil

Protein structure

Code (set theory)

Protein Data Bank (RCSB PDB)

Maximum bubble pressure method

Genetics

Sequence (biology)

Source code

Interface (matter)

MIT License

Structural bioinformatics

Protein Data Bank

Crystallography

Chemistry

Programming language

Bioinformatics

Protein-protein interactions are central to all biological processes. One frequently observed mode of such interactions is the α-helical coiled coil (CC). Thus, an ability to extract, visualize and analyze CC interfaces quickly and without expert guidance would facilitate a wide range of biological research. In 2001, we reported Socket, which locates and characterizes CCs in protein structures based on the knobs-into-holes (KIH) packing between helices in CCs. Since then, studies of natural and de novo designed CCs have boomed, and the number of CCs in the RCSB PDB has increased rapidly. Therefore, we have updated Socket and made it accessible to expert and nonexpert users alike.The original Socket only classified CCs with up to six helices. Here, we report Socket2, which rectifies this oversight to identify CCs with any number of helices, and KIH interfaces with any of the 20 proteinogenic residues or incorporating nonnatural amino acids. In addition, we have developed a new and easy-to-use web server with additional features. These include the use of NGL Viewer for instantly visualizing CCs, and tabs for viewing the sequence repeats, helix-packing angles and core-packing geometries of CCs identified and calculated by Socket2.Socket2 has been tested on all modern browsers. It can be accessed freely at http://coiledcoils.chm.bris.ac.uk/socket2/home.html. The source code is distributed using an MIT licence and available to download under the Downloads tab of the Socket2 home page.

<i>Socket2</i>: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures

Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures