Waggawagga: PDB-CoiledCoil-Prediction Statistics

Coiled-coil software comparison on PDBs (RCSB)

In order to provide insight into the study «A re-evaluation of the most commonly used coiled-coil prediction tools with respect to the most comprehensive reference data set available, the entire Protein Data Bank (PDB) [10], down to each amino acid and its secondary structure», the following platform was developed. PDB-CC, is a Web-GL based PDB-viewer for coiled-coil predictions using JSmol or ChemDoodle Web Components. PDB-CC illustrates the predictions of the most commonly used coiled-coil softwares applied to a broad data set of PDB files (state: 2018-12 with 147,073 files available), showing at which positions coiled-coil regions and the corresponding predictions are located.

Interactive statistics:

Aminoacid distribution on predicted heptad-register pattern

In the following section, you can take insight into the aminoacid distribution mapped onto the predicted heptad-register pattern of each tool. The data beyond combines all predictions made by each tool for all PDB chain sequences.

... to be continued ...

Software References

[1] Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637. DOI_disc_logo - 10.1002/bip.360221211

[2] Walshaw, J. & Woolfson, D. N. (2001). SOCKET: a program for identifying and analysing coiled-coil motifs within protein structures. J. Mol. Biol., 307(5), 1427-1450. DOI_disc_logo - 10.1006/jmbi.2001.4545

[3] Lupas, A., Dyke, M. & Stock, J. (1991). Predicting coiled coils from protein sequences. Science, 252(5009), 1162-1164. - jstor.org/stable/2876291

[4] Delorenzi, M. & Speed, T. (2002). An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics, 18, 617–625. DOI_disc_logo - 10.1093/bioinformatics/18.4.617

[5] Kim, P. S., Berger, B. & Wolf, E. (1997). MultiCoil: A program for predicting two-and three-stranded coiled coils. Protein Science, 6, 1179–1189. DOI_disc_logo - 10.1002/pro.5560060606

[6] Trigg, J., Gutwin, K., Keating, A. E. & Berger, B. (2011). Multicoil2: Predicting Coiled Coils and Their Oligomerization States from Sequence in the Twilight Zone. PLOS ONE, 6, 1–10. DOI_disc_logo - 10.1371/journal.pone.0023519

[7] Berger, B., Wilson, D. B., Wolf, E., Tonchev, T., Milla, M. & Kim, P. S. (1995). Predicting Coiled Coils by Use of Pairwise Residue Correlations. Proceedings of the National Academy of Science USA, 92, 8259-8263. DOI_disc_logo - 10.1073/pnas.92.18.8259

[8] McDonnell, A. V., Jiang, T., Keating, A. E. & Berger, B. (2006) Paircoil2: improved prediction of coiled coils from sequence. Bioinformatics, 22: 356–358. DOI_disc_logo - 10.1093/bioinformatics/bti797

[9] Naohisa Goto, Pjotr Prins, Mitsuteru Nakao, Raoul Bonnal, Jan Aerts and Toshiaki Katayama. 2010. BioRuby. Bioinformatics, 26: 2617–2619. DOI_disc_logo - 10.1093/bioinformatics/btq475

[10] Helen M. Berman, John Westbrook, Zukang Feng, Gary Gilliland, T. N. Bhat, Helge Weissig, Ilya N. Shindyalov, Philip E. Bourne. 2000. The Protein Data Bank. Nucleic Acids Research, 28: 235-242. DOI_disc_logo - 10.1093/nar/28.1.235

Rights and Restrictions

Using Waggawagga by non-academics requires permission. Waggawagga may be obtained upon request and used under a GNU General Public License.