ncoils

ncoils predicts coiled-coil secondary-structure elements in protein sequences by probabilistically comparing flanking residues to known coiled-coil proteins to assess per-residue likelihood of coiled-coil alpha-helix formation.

Key Features:

• Sequence comparison and probabilistic scoring: Assesses the probability that each residue is part of a coiled-coil by comparing its flanking sequences with those of known coiled-coil proteins.
• Identification of coiled-coil domains: Delineates coiled-coil domains in globular proteins, including recognition of leucine zipper–type regions found in transcriptional regulators.
• Detection of discontinuities within coiled coils: Predicts regions of discontinuity within coiled coils, exemplified by the hinge region in myosin.

Scientific Applications:

• Protein structure analysis: Identifies and characterizes coiled-coil domains across diverse proteins to inform structural interpretation and function.
• Functional annotation: Provides coiled-coil region predictions to support annotation of protein roles in cellular processes.
• Protein engineering and design: Identifies potential sites for modification within coiled-coil structures for engineering purposes.
• Database-scale screening (GenBank): Has been applied to proteins in GenBank, identifying over 200 proteins likely containing coiled-coil domains, including alpha- and beta-tubulins, flagellins, G protein beta subunits, some bacterial tRNA synthetases, and members of the Hsp70 family.

Methodology:

Probabilistic assessment based on sequence comparison of flanking residues with known coiled-coil proteins to determine per-residue likelihood of coiled-coil formation.