Database of Interacting Proteins

{{Short description|Database of protein interactions}}

{{infobox biodatabase

|title = Database of Interacting Proteins (DIP)

|logo = File:Database of Interacting Proteins Logo.png

|description = protein interaction database

|scope =

|organism =

|center = University of California, Los Angeles

|laboratory =

|author = David Eisenberg

|citation = Xenarios, & al. (2002){{cite journal|last1=Xenarios|first1=I|last2=Salwínski|first2=L|last3=Duan|first3=XJ|last4=Higney|first4=P|last5=Kim|first5=SM|last6=Eisenberg|first6=D|title=DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions.|journal=Nucleic Acids Research|date=Jan 1, 2002|volume=30|issue=1|pages=303–5|pmid=11752321|doi=10.1093/nar/30.1.303|pmc=99070}}

|released = 2002

|standard =

|format =

|url = http://dip.doe-mbi.ucla.edu

|download =

|webservice =

|sql =

|sparql =

|webapp =

|standalone =

|license = CC BY-ND 3.0

|versioning =

|frequency =

|curation =

|bookmark =

|version=

}}

The Database of Interacting Proteins (DIP) is a biological database which catalogs experimentally determined interactions between proteins.{{cite web|title=DIP:Home|url=http://dip.doe-mbi.ucla.edu/dip/Main.cgi|website=dip.doe-mbi.ucla.edu|accessdate=8 September 2014}}{{Cite journal

| last1 = Salwinski | first1 = L.

| last2 = Miller | first2 = C. S.

| last3 = Smith | first3 = A. J.

| last4 = Pettit | first4 = F. K.

| last5 = Bowie | first5 = J. U.

| last6 = Eisenberg | first6 = D.

| authorlink6 = David Eisenberg

| title = The Database of Interacting Proteins: 2004 update

| doi = 10.1093/nar/gkh086

| journal = Nucleic Acids Research

| volume = 32

| issue = 90001

| pages = D449–D451

| year = 2004

| pmid = 14681454

| pmc =308820

}} It combines information from a variety of sources to create a single, consistent set of protein–protein interactions. The data stored within DIP have been curated, both manually, by expert curators, and automatically, using computational approaches that utilize the knowledge about the protein–protein interaction networks extracted from the most reliable, core subset of the DIP data. The database was initially released in 2002. As of 2014, DIP is curated by the research group of David Eisenberg at UCLA.

DIP can be searched through its web interface; searches may be based on the interactions described in a selected journal article, or interactions supported by experimental evidence, amongst others.{{cite web|title=DIP:Search|url=http://dip.doe-mbi.ucla.edu/dip/Search.cgi|website=dip.doe-mbi.ucla.edu|accessdate=8 September 2014}}

DIP is a member of the International Molecular Exchange Consortium (IMEx),{{Cite journal

| last1 = Orchard | first1 = S.

| last2 = Kerrien | first2 = S.

| last3 = Abbani | first3 = S.

| last4 = Aranda | first4 = B.

| last5 = Bhate | first5 = J.

| last6 = Bidwell | first6 = S.

| last7 = Bridge | first7 = A.

| last8 = Briganti | first8 = L.

| last9 = Brinkman | first9 = F.

| last10 = Cesareni

| doi = 10.1038/nmeth.1931 | first10 = G.

| last11 = Chatr-Aryamontri | first11 = A.

| last12 = Chautard | first12 = E.

| last13 = Chen | first13 = C.

| last14 = Dumousseau | first14 = M.

| last15 = Goll | first15 = J.

| last16 = Hancock | first16 = R.

| last17 = Hannick | first17 = L. I.

| last18 = Jurisica | first18 = I.

| last19 = Khadake | first19 = J.

| last20 = Lynn | first20 = D. J.

| last21 = Mahadevan | first21 = U.

| last22 = Perfetto | first22 = L.

| last23 = Raghunath | first23 = A.

| last24 = Ricard-Blum | first24 = S.

| last25 = Roechert | first25 = B.

| last26 = Salwinski | first26 = L.

| last27 = Stümpflen | first27 = V.

| last28 = Tyers | first28 = M.

| last29 = Uetz | first29 = P.

| last30 = Xenarios | first30 = I.

| title = Protein interaction data curation: The International Molecular Exchange (IMEx) consortium

| journal = Nature Methods

| volume = 9

| issue = 4

| pages = 345–350

| year = 2012

| pmid = 22453911

| pmc =3703241

}} a group of the major public providers of interaction data. Other participating databases include the Biomolecular Interaction Network Database (BIND),{{cite journal|last1=Alfarano|first1=C.|title=The Biomolecular Interaction Network Database and related tools 2005 update|journal=Nucleic Acids Research|date=17 December 2004|volume=33|issue=Database issue|pages=D418–D424|doi=10.1093/nar/gki051|pmid=15608229|pmc=540005}} IntAct,{{cite journal|last1=Kerrien|first1=S.|last2=Aranda|first2=B.|last3=Breuza|first3=L.|last4=Bridge|first4=A.|last5=Broackes-Carter|first5=F.|last6=Chen|first6=C.|last7=Duesbury|first7=M.|last8=Dumousseau|first8=M.|last9=Feuermann|first9=M.|last10=Hinz|first10=U.|last11=Jandrasits|first11=C.|last12=Jimenez|first12=R. C.|last13=Khadake|first13=J.|last14=Mahadevan|first14=U.|last15=Masson|first15=P.|last16=Pedruzzi|first16=I.|last17=Pfeiffenberger|first17=E.|last18=Porras|first18=P.|last19=Raghunath|first19=A.|last20=Roechert|first20=B.|last21=Orchard|first21=S.|last22=Hermjakob|first22=H.|title=The IntAct molecular interaction database in 2012|journal=Nucleic Acids Research|date=24 November 2011|volume=40|issue=D1|pages=D841–D846|doi=10.1093/nar/gkr1088|pmid=22121220|pmc=3245075}} the Molecular Interaction Database (MINT),{{cite journal|last1=Zanzoni|first1=A|last2=Montecchi-Palazzi|first2=L|last3=Quondam|first3=M|last4=Ausiello|first4=G|last5=Helmer-Citterich|first5=M|last6=Cesareni|first6=G|title=MINT: a Molecular INTeraction database.|journal=FEBS Letters|date=Feb 20, 2002|volume=513|issue=1|pages=135–40|pmid=11911893|doi=10.1016/s0014-5793(01)03293-8|pmc=1751541}} MIPS,{{cite journal|last1=Guldener|first1=U.|title=MPact: the MIPS protein interaction resource on yeast|journal=Nucleic Acids Research|date=1 January 2006|volume=34|issue=90001|pages=D436–D441|doi=10.1093/nar/gkj003|pmid=16381906|pmc=1347366}} MPact, and BioGRID. The databases of IMEx work together to prevent duplications of effort, collecting data from non-overlapping sources and sharing the curated interaction data. The IMEx consortium also worked to develop the HUPO-PSI-MI XML format, which is now widely implemented.{{cite journal|last1=Hermjakob|first1=Henning|last2=Montecchi-Palazzi|first2=Luisa|last3=Bader|first3=Gary|last4=Wojcik|first4=Jérôme|last5=Salwinski|first5=Lukasz|last6=Ceol|first6=Arnaud|last7=Moore|first7=Susan|last8=Orchard|first8=Sandra|last9=Sarkans|first9=Ugis|last10=von Mering|first10=Christian|last11=Roechert|first11=Bernd|last12=Poux|first12=Sylvain|last13=Jung|first13=Eva|last14=Mersch|first14=Henning|last15=Kersey|first15=Paul|last16=Lappe|first16=Michael|last17=Li|first17=Yixue|last18=Zeng|first18=Rong|last19=Rana|first19=Debashis|last20=Nikolski|first20=Macha|last21=Husi|first21=Holger|last22=Brun|first22=Christine|last23=Shanker|first23=K|last24=Grant|first24=Seth G N|last25=Sander|first25=Chris|last26=Bork|first26=Peer|last27=Zhu|first27=Weimin|last28=Pandey|first28=Akhilesh|last29=Brazma|first29=Alvis|last30=Jacq|first30=Bernard|last31=Vidal|first31=Marc|last32=Sherman|first32=David|last33=Legrain|first33=Pierre|last34=Cesareni|first34=Gianni|last35=Xenarios|first35=Ioannis|last36=Eisenberg|first36=David|last37=Steipe|first37=Boris|last38=Hogue|first38=Chris|last39=Apweiler|first39=Rolf|title=The HUPO PSI's Molecular Interaction format—a community standard for the representation of protein interaction data|journal=Nature Biotechnology|year=2004|volume=22|issue=2|pages=177–183|doi=10.1038/nbt926|pmid=14755292|s2cid=17557764}}

All of the information within DIP is freely available under a Creative Commons BY-ND 3.0 license.