Richard Crooks's Website

bCIPA Set vs Target

Input Sequences

This tool screens the strength of interactions between all members of a single set of leucine zippers and a target sequence using the bCIPA algorithm. The original bCIPA algorithm is described by Mason et al., 2006. If you are not familiar with leucine zippers, I recommend the Wikipedia page on the subject, or if you have access, Tom Alber's 1992 review (Alber, 1992) of the motif.

Input a set of sequences to screen for interactions between

Sequences:

Allowed inputs are FASTA, a table (peptide name in left column, sequence in right column), or as one sequence per line (names assigned automatically)

Target: Name:

Frame
a: b: c: d: e: f: g:

References

Alber, T. (1992) Structure of the leucine zipper. Curr Opin Genet Dev. 2: 205-10. PubMed: 1638114

Mason, J. M., Schmitz, M. A., Müller, K. M. and Arndt, K. M. (2006) Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design. Proc Natl Acad Sci U S A. 103: 8989-94. PubMed: 16754880 - DOI: 10.1073/pnas.0509880103 - PMC: PMC1482553

Citing This Tool

If you use this tool for any published work, please cite the following
For multiple sequences:
Crooks, R. O., Lathbridge, A., Panek, A. S. and Mason, J. M. (2017) Computational Prediction and Design for Creating Iteratively Larger Heterospecific Coiled Coil Sets. Biochemistry. 56: 1573-1584. PubMed: 28267310 - DOI: 10.1021/acs.biochem.7b00047
Crooks, R. O., Baxter, D., Panek, A. S., Lubben, A. T. and Mason, J. M. (2016) Deriving Heterospecific Self-Assembling Protein-Protein Interactions Using a Computational Interactome Screen. J Mol Biol. 428: 385-398. PubMed: 26655848 - DOI: 10.1016/j.jmb.2015.11.022 - PMC: PMC4751974
For the original algorithm:
Hagemann, U. B., Mason, J. M., Müller, K. M. and Arndt, K. M. (2008) Selectional and mutational scope of peptides sequestering the Jun-Fos coiled-coil domain. J Mol Biol. 381: 73-88. PubMed: 18586270 - DOI: 10.1016/j.jmb.2008.04.030
Mason, J. M., Schmitz, M. A., Müller, K. M. and Arndt, K. M. (2006) Semirational design of Jun-Fos coiled coils with increased affinity: Universal implications for leucine zipper prediction and design. Proc Natl Acad Sci U S A. 103: 8989-94. PubMed: 16754880 - DOI: 10.1073/pnas.0509880103 - PMC: PMC1482553

Back to Biology Index
Back to Homepage