DOMMINO is a comprehensive structural database on macromolecular interactions. As of June, 2011, it contains more than 407,000 binary interactions. The distinctive features of DOMMINO are:

1. Automated updates: DOMMINO is fully automated and is designed to update itself on a weekly basis, one day after a PDB weekly update. Thus, the community will be able to study macromolecular interactions almost immediately after they are released by PDB.

2. Coverage of non-domain mediated interactions: In addition to domain-domain and domain-peptide interactions the database characterizes the interaction between domains and unstructured protein regions that are not parts of a domain, such as inter-domain linkers and N- and C-termini. The interactions that involve the latter unstructured parts of proteins have been included to the database for the first time providing additional ~186,000 interactions (~45% of the total number of interactions, as of June, 2011).

3. Coverage of new structural domains: DOMMINO employs one of the most accurate structural classifications of proteins, SCOP. In addition to the existing SCOP-annotated domains, we employ a state-of-the-art machine learning approach to classify newer protein structures into existing SCOP families. With the progress of structural genomics, we do not expect a significant growth of the number of structurally novel folds or protein families and therefore our method allows covering almost all new protein structures. In total, using this predictive approach has allowed us to add more than 261,000 new interactions, almost twice as many as existing SCOP-annotated interactions.

4. The web-interface is designed to give the user a possibility of a flexible search as well as the capability to study macromolecular interactions in a PDB structure at the interaction network level and at the individual interface level.

The web interface of the DOMMINO database includes a comprehensive list of help topics linked to the specific actions. In addition, we have designed a step-by-step tutorial that covers all aspects of working with the data from DOMMINO using the web interface.

How to cite us:
Kuang X, Han JG, Zhao N, Pang B, Shyu CR, Korkin D. "DOMMINO: A database of macromolecular interactions"; Nucleic Acids Res., (2012), 40 (database issue), D501-D506.

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