COILS

COILS predicts the likelihood that protein sequences adopt coiled-coil conformations by comparing them to a database of known parallel two-stranded coiled-coils.

Key Features:

• Sequence Comparison: Compares target protein sequences, including flanking residues, to a database of established parallel two-stranded coiled-coils.
• Similarity Scoring: Computes a similarity score quantifying how closely the target sequence resembles known coiled-coils.
• Probability Calculation: Evaluates similarity scores against score distributions from globular and coiled-coil proteins to compute the probability of coiled-coil formation.
• Domain Delineation: Identifies coiled-coil domains within otherwise globular proteins, including leucine zipper motifs in transcriptional regulators.
• Discontinuity Prediction: Predicts regions of discontinuity within coiled-coil structures, such as hinge regions relevant to proteins like myosin.

Scientific Applications:

• Structural Biology: Aids interpretation of protein architecture and function by predicting coiled-coil domains and discontinuities.
• Protein Engineering: Supports design of proteins with specified structural properties by identifying potential coiled-coil regions.
• Genomic Research: Facilitates large-scale identification of probable coiled-coil proteins (over 200 reported), including alpha- and beta-tubulins, flagellins, G protein beta subunits, bacterial transfer RNA synthetases, and members of the heat shock protein (Hsp70) family.

Methodology:

Compares sequences (including flanking residues) to a database of known parallel two-stranded coiled-coils, computes similarity scores, and evaluates those scores against distributions from globular and coiled-coil proteins to estimate per-residue and per-region coiled-coil probabilities.