Supplementary material for

Joint Evolutionary Trees : a large scale method to predict protein interfaces based on sequence sampling

S. Engelen, L.A. Trojan, S. Sacquin-Mora, R. Lavery, A. Carbone

PLoS Computational Biology, 2008. In press.

Supplementary file containing several tables:

Supplementary Tables 1-9 : Comparison of ET, JET and iJET on homodimer, heterodimer and transient interfaces of the Huang dataset.

Supplementary Table 10-13 : Size (amino-acids number) and number of sequences retrieved by PSI-BLAST for all homodimer, heterodimer and transient proteins in the Huang dataset and in an extra set of proteins discussed in the article.

Supplementary Table 14: Propensity values describing physical-chemical properties of residues at the interface as estimated in (Nagi and Braun 2007).

Supplementary Table 15-20 : iJETperformance on enzymes, inhibitor, signal transduction, antigen, antibodies, "others" proteins of the Kanamori dataset.

Supplementary Table 21-22 : Comparison of ET, JET and iJET on a set of proteins discussed in the text.

Program JET