The following resources have inspired our work and/or are used in DIMA.
We tried to reference the most relevant publications plus the respective web-sites
where possible. If you are associated with a resource, web-site, tool or publication
and feel that we should cite a different paper or site please contact us.
Pagel P, Wong P, Frishman D
A Domain Interaction Map Based on Phylogenetic Profiling J. Mol. Biol. 2004; 344(5): 1331-1346
Domain Pair Exclusion Method
Riley R, Lee C, Sabatti C, Eisenberg D.
Inferring protein domain interactions from databases of interacting proteins. Genome Biol. 2005; 6: R89
Correlated Mutation Method
OMES (Observed Minus Expected Squared) Reference:
Kass, I. and Horovitz, A.
Mapping pathways of allosteric communication in GroEL by analysis of correlated mutations. Proteins.2002; 48: 611-617
ELSC (Explicit Likelihood of Subset Covariation) Reference:
Dekker, J. P.; Fodor, A.; Aldrich, R. W. and Yellen, G.
A perturbation-based method for calculating explicit likelihood of evolutionary co-variance in multiple sequence alignments. Bioinformatics. 2004; 20: 1565-1572
Olmea, O. and Valencia, A.
Improving contact predictions by the combination of correlated mutations and other sources of sequence information. Fold Des. 1997; 2: S25-S32
Domain Interaction Prediction in a Discriminative Way
Zhao, X.-M., Chen, L. and Aihara, K.
A discriminative approach for identifying domain-domain interactions from protein-protein interactions. Proteins. 2010; 78: 1243-1253
Finn RD, Marshall M, Bateman A.
iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics. 2005;21:410-2
Rattei, T. et al.
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters. Nucleic Acids Res. 2010; 38: D223-D226
Ng SK, Zhang Z, Tan SH, Lin K.
InterDom: a database of putative interacting protein domains for validating predicted protein interactions and complexes. Nucleic Acids Res. 2003; 31: D251-254.