Richard Crooks's Website

bCIPA Set Vs Set Screener

Input Sequences

This tool screens the strength of interactions between all members of one set of leucine zippers and another set of leucine zippers 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 two sets sequences and screen all interactions between one set and the other

Sequences Set 1:

Sequences Set 2:

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

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

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