Socket2: a program for locating, visualizing and analyzing coiled-coil interfaces in protein structures
Open accessAbstract
Motivation: 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. Results: 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. Availability and implementation: 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.
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CC+ can generate search-specific data on the fly, including position-specific scoring matrices (PSSMs) from the selected sequences; and models of the CC regions in context of the whole protein structure.
“Third, following user‐defined searches, CC+ can generate search‐specific data on the fly, including: position‐specific scoring matrices (PSSMs) from the selected sequences; and models of the CC regions in context of the whole protein structure, which can be visualized and interrogated using the interactive GUI of Socket2 (Kumar & Woolfson, 2021).”
From <scp> CC <sup>+</sup> </scp> : A searchable database of validated coiled coils in <scp>PDB</scp> structures and <scp>AlphaFold2</scp> models (2023) · cites this paper as Kumar & Woolfson, 2021
There are some very large CC assemblies with >6 helices, which Socket2 can now identify.
“Interestingly, there are some very large CC assemblies with >6 helices, which Socket2 can now identify (Kumar & Woolfson, 2021).”
From <scp> CC <sup>+</sup> </scp> : A searchable database of validated coiled coils in <scp>PDB</scp> structures and <scp>AlphaFold2</scp> models (2023) · cites this paper as Kumar & Woolfson, 2021
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“Here, the figure and the PDB ID act as a clickable links to an interactive GUI running Socket2 (Kumar & Woolfson, 2021) to visualize and download images of that CC.”
BackgroundMethodInfluentialSelf-citation
- Authors
- Kumar, P., & Woolfson, D. N.
- Affiliations
- University of Bristol (GB)
- Corresponding author
- Kumar, Prasun
- Woolfson, Derek N
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2021-09-08
- Volume
- 37
- Issue
- 23
- Pages
- 4575-4577
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC8652024
- OpenAlex
- W3198143332
- Cited by
- 51
- References
- 3
- Citations by year
- 2026: 5 · 2025: 7 · 2024: 11 · 2023: 13 · 2022: 14 · 2021: 1
- FWCI
- 3.06
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Bioinformatics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Explore Bristol Research (acceptedVersion, cc-by)
- Bristol Research (University of Bristol) (submittedVersion, cc-by)
- Funders
- Biotechnology and Biological Sciences Research Council (BB/R00661X/1)
- BrisSynBio
- Synthetic Biology Research Centre (BB/L01386X/1)
- Royal Society Wolfson Research Merit Award (WM140008)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
- Keywords
- coiled coil, protein-protein interaction, protein structure analysis, helix packing, web server, NGL viewer, sequence repeats, unnatural amino acids
- MeSH terms
- Protein Domains, Protein Conformation, alpha-Helical, Proteins, Software, Protein Structure, Secondary
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