Capturing cooperative interactions with the PSI-MI format

Database (Oxford). 2013 Sep 25;2013:bat066. doi: 10.1093/database/bat066. Print 2013.

Abstract

The complex biological processes that control cellular function are mediated by intricate networks of molecular interactions. Accumulating evidence indicates that these interactions are often interdependent, thus acting cooperatively. Cooperative interactions are prevalent in and indispensible for reliable and robust control of cell regulation, as they underlie the conditional decision-making capability of large regulatory complexes. Despite an increased focus on experimental elucidation of the molecular details of cooperative binding events, as evidenced by their growing occurrence in literature, they are currently lacking from the main bioinformatics resources. One of the contributing factors to this deficiency is the lack of a computer-readable standard representation and exchange format for cooperative interaction data. To tackle this shortcoming, we added functionality to the widely used PSI-MI interchange format for molecular interaction data by defining new controlled vocabulary terms that allow annotation of different aspects of cooperativity without making structural changes to the underlying XML schema. As a result, we are able to capture cooperative interaction data in a structured format that is backward compatible with PSI-MI-based data and applications. This will facilitate the storage, exchange and analysis of cooperative interaction data, which in turn will advance experimental research on this fundamental principle in biology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Allosteric Regulation
  • Cell Cycle Proteins / chemistry
  • Cyclin A / chemistry
  • Cyclin-Dependent Kinase 2 / chemistry
  • Databases, Protein*
  • Humans
  • Models, Molecular
  • Molecular Sequence Annotation
  • Phosphorylation
  • Protein Binding
  • Protein Interaction Mapping*
  • Proteomics*

Substances

  • Cell Cycle Proteins
  • Cyclin A
  • Cyclin-Dependent Kinase 2