structure-based prediction of protein complexes
MODTIE predicts binary protein interactions and higher-order protein complexes from a set of protein sequences based on their similarity to template complexes of known structure. It can be used for genome-wide prediction, through interaction with the MODBASE database of comparative models, or to score individual protein complexes. This software has been previously used in the prediction of protein interactions in S. cerevisiae and host-pathogen protein interactions betwen human and ten pathogens.
The latest release of MODTIE (v1.11) uses template structures from PIBASE v2010 and domain definitions from SCOP v1.75.
This package includes a users manual that describes how to install and run the software.
If you use the software to predict protein interactions within a single species, or to score protein complexes, please cite:
Protein complex compositions predicted by structural similarity.
Davis FP, Braberg H, Shen MY, Pieper U, Sali A, Madhusudhan MS. Nucleic Acids Res (2006) 34:2943-2952.
http://nar.oxfordjournals.org/cgi/content/full/34/10/2943
If you use the software to predict inter-species protein interactions, such as host--pathogen interactions, please cite:
Host-pathogen protein interactions predicted by comparative modeling.
Davis FP, Barkan DT, Eswar N, McKerrow JH, Sali A. Protein Sci (2007) 16:2585-2596.
http://www.proteinscience.org/cgi/doi/10.1110/ps.073228407