The DIPTM
(Database of Interacting Proteins) database lists protein pairs that are
known to interact with each other. By interact we mean that two
amino acid chains were experimentally identified to bind to each other.
The database lists such pairs to aid those studying a particular
protein-protein interaction but also those investigating entire regulatory
and signaling pathways as well as those studying the organisation and
complexity of the protein interaction network at the cellular level.
The DIP database is composed of nodes and edges:
DIP Nodes (proteins)
Each protein participating in a DIP interaction
is idetified by a unique identifier of the form
<DIP:nnnN> and cross-references to, at least,
one of the major protein databases -
PIR,
SWISSPROT and/or
GENBANK
In addition, some basic information about each protein, such as name,
function, subcellular localization and cross-references to other biological
databased is stored locally (if available) in case the cross-referenced
databases are not accessible.
DIP Edges (interactions)
The information about each DIP interaction is
identified by a unique identifier of the form
<DIP:nnnE> that provides access to information
such as the region involved in the interaction, the dissociation constant
and the experimental methods used to identify and characterize the
interaction.
The DIP database can be searched in a number of ways in order to identify the starting
point for exploration of the protein interaction network. Please, see
for detailes.
DIP node ID
This is a unique identifier for each protein
described within the DIP database. It has a format
<DIP:nnnN>.
Description/Name
The common name of the proten and/or
its short description.
Primary Database reference(s)
At least one reference to PIR, SWISSPROT and/or
GENBANK entry is provided.
Cross-references
Rreferences to other database entries related to
the protein of interest as retrieved from SwissProt and NR BLAST entries.
The list of cross-references is subdivided into (P)rotein, (D)omain and
(F)eature (eg motifs) categories.
Superfamily
The superfamily specified in the PIR entry.
Organism
The organism producing the protein. A
cross-reference to the TaxonID database is provided for additional
information.
Function
A short description of the protein's function
within the cell.
Localization
Localization of the protein within the cell (if
known)
Keywords
Keywords associated with the protein. They might
describe its structure and/or sequence features, biological activity,
function, cellular localization, etc.
DIP interaction ID
This is a unique identifier for each interaction
described within the DIP database. It has a format
<DIP:nnnE>. For example,
DIP:1234E referes to the interaction between actin and foofoo in
S. cerevisiae. Please, use the DIP interaction ID when referring
to an interaction described within the DIP database.
Residue Ranges
The range is meant to specify more accurately which
parts of the proteins are directly involved in the interaction.
Protein Domain
The interacting domain name. An incomplete list of
domain names
is available.
Dissociation Constant
The dissociation constant of the protein-protein
complex in mols/liter (M).
Experimental Method(s)
The experimental method(s) used to identify and/or
characterize the interaction.
Reference(s)
A literature reference to the experimental work
studying the interactions.
Comments
Additional comments supplied by the person who
deposited the interaction. Comments could include an explanation
(evidence) why the proteins are thought to interact, and what the
biological significance of the interaction is.
If you know of an interaction but do not want to look for the unique
Id's, or don't want to submit it for some other reason, or if you know of
a protein-protein interaction where the PIR/SWISSPROT/GENBANK file for one
or both of the proteins is not yet available please
email us with the names of the two
proteins and any other information you would like to include. Thanks.
For help on finding the Id for a protein go to for PIR accession code
or to for SWISSPROT code and for
NCBI/EMBL gi.
One of these code (PIR/SWISSPROT) is nececessary to enter a new protein
protein interaction.
DIPTM is updated via the web by, both professional curators,
as well as by volunteers. One doesn't have to be the discoverer of the
interaction to make a submission - it's enough to provide us with the pair
of interacting proteins and a reference to an experiment identifying the
interactions.
Last modified: Mon Dec 31 14:43:42 PST 2001
