SOCKET

SOCKET identifies coiled-coil motifs in protein structures by detecting the characteristic "knobs-into-holes" side-chain packing to define helix-helix interactions.

Key Features:

• Coiled-coil identification: Recognizes the knobs-into-holes side-chain packing pattern to automatically identify coiled-coil structures within protein data.
• Helix boundaries and oligomerization: Determines helix boundaries, oligomerization state, strand number and orientations such as parallel or anti-parallel assemblies, including two-, three-, four-stranded coiled coils and parallel pentamers.
• Heptad register assignment: Assigns heptad registers to identified motifs and highlights core residues important for sequence-structure relationships.
• PDB-derived structural database and analyses: Compiles a set of unambiguous coiled-coil structures from the RCSB Protein Data Bank to support structural and sequence analyses.
• Amino-acid profiling: Generates detailed amino acid profiles for heptad repeats across different coiled-coil motifs.

Scientific Applications:

• Coiled-coil diversity and function: Enables study of amino-acid preferences and variation across heptad repeats to investigate coiled-coil diversity and functionality.
• Protein-protein interaction and motif design: Supports analysis of coiled-coil assembly principles and provides data useful for prediction and design of coiled-coil motifs and protein-protein interaction studies.

Methodology:

Detection of knobs-into-holes side-chain packing to identify coiled coils; assignment of heptad registers and core residues; determination of helix boundaries, strand number, orientation and oligomerization state; and compilation of identified coiled-coil structures from the RCSB Protein Data Bank for structural and sequence analyses.