BIS² co-evolution analysis of DENV envelope glycoproteins

Here we provide the files used and produced in our co-evolution analysis performed on the envelope glycoproteins E and PrM of the Dengue Virus (DENV), serotype 2.

Each folder contains the results of the co-evolution analysis performed with BIS²:

• Sequence alignments used as input (FASTA format), for E and PrM-E.
• A visualization of the alignment and the detected clusters for E and E-PrM-E.
  In each cluster, hits are marked by the letter "H". The "E" letters refer to hit extensions, which are not used in our analysis. The lowercase "x" mark the presence of another hit further in the sequence, thus they are only there to help visualization but do not contain information.
• A schematic visualization of the alignment and the detected clusters for E and PrM-E.
  Only the hits are shown.
• List of clusters produced by the analysis with residue variations, for E and PrM-E.
  The positions given in these tables refer to alignment columns in the corresponding alignment.
• Same as above, in text format.
  This is useful for parsing BIS² results for further analysis steps. Text format contains p-values for each cluster.
• Chimera session with mapping of BIS² clusters on 3D structures.
  Mapping is done on three pdb structures: 1K4R, 36CR, 3IXY. Only significant BIS² clusters are shown (p-value ≤ 0.05). Note that some clusters map outside the PDB sequence, thus they are not reported.

⚠ Note that the order of the clusters in the article (see below) and in the files provided in this webpage might differ. Please be aware of this when referring to cluster's IDs.

Contacts

For questions, comments, or suggestions on BIS/BIS² co-evolution analysis, feel free to contact Alessandra Carbone or Francesca Nadalin.

For questions, comments, or suggestions regarding DENV biology, feel free to contact Dimitri Lavillette or Florian Douam.

References

The results reported in this webpage are described in the following article:

• F. Douam, et al. A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism. (under review)

The description of BIS/BIS² co-evolution method can be found in the following articles:

• F. Oteri, F. Nadalin, R. Champeimont, A. Carbone, BIS2Analyzer: a server for co-evolution analysis of conserved protein families, Nucleic Acids Research, 45(W1): W307–W314, 2017.
  ⇨ to the webserver
• L. Dib, A. Carbone. Protein fragments: functional and structural roles of their coevolution networks, PLoS ONE, 7(11): e48124, 2012.

Last Update October 2017