DIP Overview

Database Contents

The DIP Database keeps track of experiments demonstrating protein-protein interactions that have been published in peer-reviewed, primary research articles. This unstructured, free-text information is manually converted by the DIP curators into structured database records that are amenable to computational processing and analysis. The resulting records are entered into our database system, cross-referenced to other biological resources and organized into a human-searchable on-line resource. At the same time various sets of the database records are provided for downloading and further computational analysis.

Identifying interacting molecules

The molecules within DIP - proteins and peptides - are most often identified by providing cross-references to at least one of the well-established protein sequence database - typically UniprotKB or RefSeq. In case of proteins not yet annotated by UniprotKB or RefSeq a reference to a gene or protein within one of the organism-specific genome databases might be used. Shorter peptides with sequences common to multiple proteins are often characterized by simply providing their sequence. Each molecule record within DIP might correspond to a collection of...

Classifying interactions

Depending on the strength of the available experimental evidence, interactions between proteins may be classified according to the detected level of contact between the interacting proteins. Thus, interactions may be reported as:
  • direct interactions, if the interacting proteins are known touch each other directly;
  • physical associations, if the proteins physically associate, with the possibility that another molecule mediates the association; or
  • associations, if the proteins were simply copurified but with the experimental evidence not strong enough to demonstrate that every two proteins within the group physically associate. Most often, molecules forming association are co-purified by a pull-down or coimmunoprecipitation and share the same bait molecule.

In addition, pairs of proteins or genes may be reported as participating in:

  • functional linkages, if the proteins (or genes) are linked by a related function, regardless of whether they physically associate; or
  • genetic interactions that are observed between genes when two genetic perturbations (e.g. gene mutations) have a combined phenotypic effect not caused by either perturbation alone.

The DIP Database currently records direct and physical interactions as well as protein associations. For functional interactions, try our ProLinks site.

NOTE: It is of utmost importance to understand the differences between various interactions types reported by the DIP and ProLinks databases. Improper interpretation of the interaction data can result in numerous misunderstandings and errors. Please, check our tnteraction typescontact us.

Interaction Networks

Conventionally, interactions between proteins are often represented by nodes (circles) and edges (lines), both combined into a mathematical object called a graph:

(kinetochore network graph) The graph on the left shows a part of the protein-protein interaction network of the kinetochore, the protein complex responsible for separating chromosomes during eukaryotic cell division. Notice that some of the edges, the curved ones, indicate a self interaction: an interaction between a protein and another copy of itself.