Instructions for bZIP Coiled-Coil Scoring Form


Example: If the form is left blank, clicking "submit" shows sample output on a segment of the human C/EBPepsilon homodimer with the default sequences and registers.

Required input: Two aligned protein sequences and their assigned register. The sequences should be a string of amino acid 1-letter abbreviations. The registers should be a string of characters a through g. Note that this program has only been tested for coiled coils with uninterrupted register.

Sequence and register length:

Additional fine print:


The program will terminate with a message under the following situations: However, it will not check if your input is a valid coiled-coil sequence! To detect coiled-coil motifs in a sequence, please use the PairCoil or MultiCoil programs.

If all output scores are 0, there is an error in the input.

Interpreting the output

For error checking, the original input is displayed, as well as the trucated sequences and registers used for scoring.

Scores are computed using four classification models:

Higher scores correspond to more likely interactions.

Actual scores computed using the above weights are shown for the sequence1+sequence2 interaction.

Scores for each sequence may vary according to its amino-acid composition; therefore, for reference the distribution of scores for sequence1, paired with each bZIP sequence in a dataset of 8 genomes, is shown. Likewise for sequence2.

The percentile is computed as the number of pairings that score worse than the sequence1+sequence2 score, divided by total number of pairings across all genomes. Pairings are taken using either sequence1 or sequence2. (Note that sequence1+sequence2 is scored using the given alignment, but they are individually aligned optimally with all the other bZIPs and then scored following the new alignment.)

Cross-genomic bZIP dataset

Sequence1 is aligned with bZIP coiled-coil sequences from

Genome Number of sequences
Anopheles gambiae (mosquito) 23
Arabidopsis thalania 77
Caenorhabditis elegans (worm) 25
Drosophila melanogaster (fly) 29
Danio rerio (zebrafish) 51
Fugu rubripes (fugufish) 54
Homo sapiens (human) 53
Saccharomyces cerevisiae (yeast) 16

The mouse and rat genomes were omitted because of near identity to the human genome.