SOCKET, Woolfson Group, University of Bristol
The SOCKET program finds the Knobs-into-Holes mode of packing between alpha-helices (Crick, 1953) which is characteristic of coiled coils. It unambiguously defines the beginning and end of coiled-coil motifs in protein structures and assigns a heptad register to the sequence, highlighting the core-residues with a RasMol script (Sayle & Milner-White, 1995) if required.
This type of packing is arguably the simplest and most regular kind of tertiary and quaternary interaction which occurs in proteins; yet the sequences and architectures of coiled coils are reasonably diverse, despite sharing the same packing characteristics . A better understanding of the relationship between the sequence and structure of this motif has implications not just for the design of new coiled coils and their recognition in protein sequences, but also for the prediction of quaternary-interactions between proteins.
Specifically, the purposes of SOCKET are:
- Crick, F.H.C. (1953) Acta Cryst. 6 689-697
- Sayle, R. & Milner-White E.J. Trends in Biochemical Sciences 20 (9) 374
- Walshaw, J. & Woolfson, D.N. (2001) J. Mol. Biol., 307 (5), 1427-1450