Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures
— University of Bristol Skip to main navigation Skip to search Skip to main content University of Bristol Home Help & Terms of Use Home Profiles Research Units Research Outputs Projects Student theses Datasets Activities Prizes Facilities/Equipment Search by expertise, name or affiliation Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures Prasun Kumar, Derek N Woolfson School of Chemistry The Bristol Centre for Nanoscience and Quantum Information Synthesis Soft Matter, Colloids and Materials Catalysis Biological and Archaeological Chemistry Research output: Contribution to journal › Article (Academic Journal) › peer-review Overview Fingerprint Abstract 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. Original language English Journal Bioinformatics Early online date 8 Sep 2021 DOIs https://doi.org/10.1093/bioinformatics/btab631 Publication status Published - 8 Sep 2021 Access to Document 10.1093/bioinformatics/btab631 Full-text PDF (final published version) This is the final published version of the article (version of record). It first appeared online via Oxford University Press at 10.1093/bioinformatics/btab631. Please refer to any applicable terms of use of the publisher. Final published version, 558 KBLicence: CC BY Fingerprint Dive into the research topics of 'Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures'. Together they form a unique fingerprint. Protein Structure Mathematics 100% Coil Mathematics 96% Helix Mathematics 88% Licensure Medicine & Life Sciences 78% Biological Phenomena Medicine & Life Sciences 70% Knobs Engineering & Materials Science 67% Proteins Engineering & Materials Science 65% Packing Mathematics 52% View full fingerprint Cite this APA Author BIBTEX Harvard Standard RIS Vancouver Kumar, P., & Woolfson, D. N. (2021). Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures. Bioinformatics. https://doi.org/10.1093/bioinformatics/btab631 Kumar, Prasun ; Woolfson, Derek N. / Socket2 : A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures. In: Bioinformatics. 2021. @article{0b0b1dc2a3c54661b8d916a0d920a521, title = "Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures", abstract = "MotivationProtein–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.ResultsThe 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 implementationSocket2 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.", author = "Prasun Kumar and Woolfson, {Derek N}", year = "2021", month = sep, day = "8", doi = "10.1093/bioinformatics/btab631", language = "English", journal = "Bioinformatics", issn = "1367-4803", publisher = "Oxford University Press", } Kumar, P & Woolfson, DN 2021, 'Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures', Bioinformatics. https://doi.org/10.1093/bioinformatics/btab631 Socket2 : A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures. / Kumar, Prasun; Woolfson, Derek N. In: Bioinformatics, 08.09.2021. Research output: Contribution to journal › Article (Academic Journal) › peer-review TY - JOUR T1 - Socket2 T2 - A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures AU - Kumar, Prasun AU - Woolfson, Derek N PY - 2021/9/8 Y1 - 2021/9/8 N2 - MotivationProtein–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.ResultsThe 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 implementationSocket2 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. AB - MotivationProtein–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.ResultsThe 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 implementationSocket2 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. U2 - 10.1093/bioinformatics/btab631 DO - 10.1093/bioinformatics/btab631 M3 - Article (Academic Journal) C2 - 34498035 JO - Bioinformatics JF - Bioinformatics SN - 1367-4803 ER - Kumar P, Woolfson DN. Socket2: A Program for Locating, Visualising, and Analysing Coiled-coil Interfaces in Protein Structures. Bioinformatics. 2021 Sep 8. https://doi.org/10.1093/bioinformatics/btab631 Powered by Pure, Scopus & Elsevier Fingerprint Engine™ © 2021 Elsevier B.V. We use cookies to help provide and enhance our service and tailor content. By continuing you agree to the use of cookies Log in to Pure University of Bristol data protection policy About web accessibility
