Socket: a program for identifying and analysing coiled-coil motifs within protein structures.
By J. Walshaw, Derek N. Woolfson. Journal of Molecular Biology, 2001
356 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/8f88102ee81c59d9e0be7271ec9bed9028086e18
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- Johannes Söding
- Andrei N. Lupas
- Markus Gruber
- Christopher W. Wood
- Lukasz Kurgan
- Terence P. Speed
- Mauro Delorenzi
- Bonnie Berger
In Molecular Biology
- Andrei N. Lupas
- Johannes Söding
- Bonnie Berger
- Lukasz Kurgan
- Ke Chen
- Mauro Delorenzi
- Markus Gruber
- Amy E. Keating
Citations in the corpus
- Computational design of water-soluble α-helical barrels (2014, methodology): “This uses Crick’s equations to build coiled-coil backbones (11, 12), adds side chains using SCRWL (26) and PyRosetta (27), and assesses inter-helix packing through implementations of the BUDE forcefield (25, 28) and SOCKET (29).”
- 2018). CCBuilder 2.0: Powerful and accessible coiled-coil modeling (2017, methodology): “and a modern implementation of the SOCKET protocol.(48) The BUFF module in ISAMBARD provides an Figure 3.”
- Comparative analysis of coiled-coil prediction methods. (2006, methodology): “Only sections that were clearly identiWed as being engaged in knobs-into-holes packing were considered (superfamilies h.4.10, h.4.11, h.4.14, h.4.16, and h.6.1 were thus excluded, since SOCKET could not Wnd this packing in any member structure).”
- An HMM model for coiled-coil domains and a comparison with PSSM-based predictions (2002, methodology): “A tool called SOCKET, which could prove very helpful in setting up such a database, has been recently described (Walshaw and Woolfson, 2001).”
- Structural insights into the assembly of the histone deacetylase-associated Sin3L/Rpd3L corepressor complex (2015, methodology): “The structure was analyzed using SOCKET (62), HELANAL-Plus (63), and MONSTER (50) webservers.”
- Computational prediction of secondary and supersecondary structures. (2013, background): “The coiled coils are usually assigned with the SOCKET program (88), which locates/annotates coiled-coil interactions based on the distances between multiple helical”
- Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone (2011, methodology): “The complete database was named NPS (for New families, Paircoil2, SOCKET).”