DIMA – Links

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.

Data and resources used by DIMA

DIMA uses the following tools and resources.

Domain Phylogenetic Profiling

Reference:
Pagel P, Wong P, Frishman D
A Domain Interaction Map Based on Phylogenetic Profiling
J. Mol. Biol. 2004; 344(5): 1331-1346
doi: 10.1016/j.jmb.2004.10.019

Domain Pair Exclusion Method

Reference:
Riley R, Lee C, Sabatti C, Eisenberg D.
Inferring protein domain interactions from databases of interacting proteins.
Genome Biol. 2005; 6: R89
doi: 10.1186/gb-2005-6-10-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
doi: 10.1002/prot.10180

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
doi: 10.1093/bioinformatics/bth128

McBASC
Reference:
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
doi: 10.1016/S1359-0278(97)00060-6

Domain Interaction Prediction in a Discriminative Way

Reference:
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
doi: 10.1002/prot.22643

iPFAM

Weblink: http://www.sanger.ac.uk/Software/Pfam/iPfam/

Reference:
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
doi: 10.1093/bioinformatics/bti011

3did

Weblink: http://3did.irbbarcelona.org/

Reference:
Stein A, Panjkovich A, Aloy P
3did Update: domain-domain and peptide-mediated interactions of known 3D structure.
Nucleic Acids Res. 2009; 37:D300-D304
doi: 10.1093/nar/gkn690

IntAct

Weblink: http://www.ebi.ac.uk/intact/

Reference:
Aranda, B. et al.
The IntAct molecular interaction database in 2010.
Nucleic Acids Res. 2010; 38:D525-31
doi: 10.1093/nar/gkp878

STRING

Weblink: http://string.embl.de

Reference:
Jensen, L. J. et al.
STRING 8--a global view on proteins and their functional interactions in 630 organisms.
Nucleic Acids Res. 2009; 37:D412-6
doi: 10.1093/nar/gkn760

SIMAP

Weblink: http://mips.gsf.de/genre/proj/simap

Reference:
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
doi: 10.1093/nar/gkp949

Cytoscape Web

Weblink: http://cytoscapeweb.cytoscape.org/

Reference:
Lopes CT. et al.
Cytoscape Web: an interactive web-based network browser.
Bioinformatics. 2010 Jul 23.
doi: 10.1093/bioinformatics/btq430

Other Resources of interest

The following resources are not part of DIMA but may be of interest.

PFAM

Excellent database of conserved protein domains
Weblink: http://pfam.sanger.ac.uk/

Reference:
The Pfam protein families database
Finn, R. D. et al.
Nucleic Acids Research. 2010; Database Issue 38:D211-D222
doi: 10.1093/nar/gkp985

InterPro

A meta database integrating many different protein domain resources
Weblink: http://www.ebi.ac.uk/interpro/

Reference:
Hunter, S. et al.
InterPro: the integrative protein signature database.
Nucleic Acids Res. 2009; Database Issue 37: D211-D215.
doi: 10.1093/nar/gkn785

InterDom

Another database of domain interactions with a different approach
Weblink: http://interdom.i2r.a-star.edu.sg/

Reference:
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.