InterMap3D predicts interacting protein residues by identifying co-evolving pairs of aminoacids from an alignment of protein
sequences. The only required input is a single protein sequence in fasta format, but using a manually curated alignment is advised. If you nevertheless only input a single protein sequence, then an alignment will be generated automatically and, unless you choose another option, realigned with MAFFT. We advise caution in interpreting results from an automatically generated alignment, and that the user examines the alignment itself.
Once an alignment is available (either provided by the user or automatically generated), it is used for detecting coevolving positions, which can be done by one or more of the following three methods: "RCW MI", "MI/Entropy" and "Dependency". Moreover, by selecting more than one method (checking in more than one checkbox) one can obtain the intersection of the predictions of 2 or 3 methods. This can be helpful in obtaining more robust predictions. To obtain each method's predictions separately, one should run the server several times, one for each method.
These predicted positions are then depicted on the 3D structure of the protein most similar to yours available in the PDB database.
If you mouse-over the options, you will get a short explanation box. For a more detailed explanation, please refer to the instructions page.
InterMap3D: visualizing predicted co-evolving protein residues. R. Gouveia-Oliveira, F. Roque, R. Wernersson, T. Sicheritz-Ponten, P. W. Sackett, A. Mølgaard, A. G. Pedersen. Bioinformatics,Vol. 25, no. 15, 2009, pages 1963-1965. Download full article.
As well as any of the ones below you may have used:
RCW MI: Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation R. Gouveia-Oliveira, A. G. Pedersen. Algorithms in Molecular Biology 2007 Oct 3;2(1):12 .
MI/ENTROPY: Using information theory to search for co-evolving residues in proteins. L. C. Martin, G. B. Gloor, S. D. Dunn and L. M. Wahl Bioinformatics,Vol. 21, no. 22, 2005, pages 4116-4124
DEPENDENCY: Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments. Elisabeth R. M. Tillier and Thomas W. H. Lui Bioinformatics,Vol. 19, 2003, pages 750-755
As new methods are added, additional references to be cited will be placed here.
InterMap3D allows the introduction of new methods for predicting co-evolving residues. If you have developed a method in this area and would like to see it integrated with InterMap3D, please write us by email to email@example.com.
This file was last modified Tuesday 1st of December 2009 17:14:29 GMT