Exploiting the co-evolution of interacting proteins to discover interaction specificity

Predicting interaction specificity, such as matching members of a ligand family to specific members of a receptor family, is largely an unsolved problem. This tool utilizes evolutionary relationships within and between such families to to predict their physical interaction. This essentially aligns phylogenetic trees of interacting protein families to define the partners. The prediction accuracy depends strongly on the complexity of the phylogenetic trees as measured using information theortic methods.

More information can be obtained from JMB 2003; 327(1):273-284.here

NOTE:
1. Please make sure that the files are in Fasta Format.
2. The number of sequences in the two files should be equal.

 
THE STEPS IN THE PROCESS ARE:
  1. Upload the two files that contain the amino acid sequences of the protein families to be compared
  2. The algorithm carries out a multiple sequence alignment using Clustalw1.7
  3. You can either run the matrix alignment on our server right away and the results will be mailed to you or you can download the files for later analysis
  4. Specify the number of runs you wish to carry out.
  5. The results in the form of a table, with accuracy etc will be mailed to you.
NEW : Programs for download i have added the simulated annealing and its associated programs for download.

For obtaining the distance matrices you would have to EITHER use your own multiple sequence alignment program OR the output of the sequence alignment from this website (uses clustalw1.7), before running the simulated annealing programs locally on your machines.




Copyright © 2002, 2003, Arun Ramani and Edward Marcotte. The MATRIX server is the property of the University of Texas, and cannot be used for commercial purposes without written permission of Edward Marcotte and the University of Texas. It is forbidden to redistribute, derivatize, or encapsulate the protein link explorer data or server in another database without permission. Sale of information derived from it, whether directly or in revised form, is forbidden except by permission of UT and Edward Marcotte. All copies or mirrors of the MATRIX must carry this notice.

mail any questions or comments to arun at icmb dot utexas dot edu