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专业背景:计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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蛋白质相互作用数据库  

2011-01-18 14:33:31|  分类: 计算系统生物学 |  标签: |举报 |字号 订阅

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Protein–protein interaction prediction

http://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction_prediction

 

蛋白质间的相互作用是研究生物反应机制的重要工具。目前有两个主要的数据库收录这类信息,DIP(http://dip.doe-mbi.ucla.edu/) 与 BIND(http://www.bind.ca/)。

DIP 可以用基因的名字等关键词查询,使用上较方便。查询的结果列出节点 (node) 与连结 (link) 两项,节点是叙述所查询的蛋白质的特性,包括蛋白质的功能域(domain)、指纹(fingerprint) 等,若有酶的代码或出现在细胞中的位置,也会一并批注。连结所指的是可能产生的相互作用,DIP 对每一个相互作用都会说明证据(实验的方法)与提供文献,此外,也记录除巨量分析外,支持此相互作用的实验数量。DIP 还可以用序列相似性(使用Blast)、模式 (pattern) 等查询。至2002 年6 月,已收录了约一万八千个蛋白质间的相互作用信息条目。

BIND 所收录的资料较少,不过其呈现的信息方式比DIP 要实用,除了记录相互作用条目外,还特别区分出其中的一些复合物及其反应路径。因为复合物与反应路径中含有多种相互作用,所以至2002 年11 月就收录有的相互作用总数约一万一千多条。在BIND 中所纪录的内容与DIP 相似,包括蛋白质的功能域、在细胞中表达的位置等。对于蛋白质间的相互作用,以文字叙述的方式呈现证据,并提供文献的链接。BIND 这种区分出复合物与路径的作法,让使用者能节省许多解读数据的精力,这是比DIP 强的地方;在查询接口上,除了可以用关键词、序列相似性等搜寻外,还允许使用者浏览数据库中所有的资料。BIND 在收录资料时主要是利用文献,他们提供PreBIND 这个工具,使用者可用PreBind 浏览他们正在处

理的一些可能的交互作用,所提供的文献链接,让使用者可自行判断所寻求的相互作用是否为真。

PubGeneTM是一个文献数据库,收录可能有关的基因或其蛋白质产物。它利用的假设是:两个基因的名字若出现在同一篇文章内,就可能代表它们相关,因此计算同时出现某两个基因名字的文章篇数,可作为其收录的准则。这个数据库分别收录了人类、小鼠、大鼠中,已知基因的所有两两组合。虽然这样的作法,无法精确地区分两个基因是因为出现在基因组上的邻近位置,或是有相似的基因表达模式,或是蛋白质间可能有的相互作用,却可有助于使用者研究感兴趣但在DIP、BIND 中找不到的蛋白质。

PubGeneTM 的镜相站 (http://ref.ym.edu.tw/pubgene/)

 

 

蛋白质相互作用数据库 - fhqdddddd - 流浪云南

 
DIP - Db of Interacting Proteins
INTERACT - Protein-Protein interaction db
ProNet - Protein-Protein interaction db
CANSITE - Signal Transduction‘s (信号传导)Web
SPAD - Signaling pathway db
CSNDB - Cell Signaling Networks db 
 
DPInteract - DNA-Proteins interactions db


植物方面

http://www.plapid.org/

http://www.geneinfinity.org/sp_proteininteraction.html

 

Construction and analysis of protein-protein interaction networks. Raman K. Autom Exp. 2010 Feb 15; 2(1):2. Epub 2010 Feb 15. [Autom Exp. 2010]
Data integration and exploration for the identification of molecular mechanisms in tumor-immune cells interaction. Mlecnik B, Sanchez-Cabo F, Charoentong P, Bindea G, Pagès F, Berger A, Galon J, Trajanoski Z. BMC Genomics. 2010 Feb 10; 11 Suppl 1:S7. Epub 2010 Feb 10. [BMC Genomics. 2010]


Protein-protein interactions:
STRING: a database of predicted functional associations between proteins. PMID: 12519996
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 2005 Jan 1; 33(Database issue):D433-7. [Nucleic Acids Res. 2005]
STRING 8 a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res. 2009 Jan; 37(Database issue):D412-6. Epub 2008 Oct 21. [Nucleic Acids Res. 2009]
STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003 Jan 1; 31(1):258-61. [Nucleic Acids Res. 2003]
STRING: functional protein association networks
http://string-db.org/         (推荐)

 

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. PMID: 11752321 http://dip.doe-mbi.ucla.edu      (推荐)

 

The IntAct Molecular Interaction database. PMID: 11752321 http://www.ebi.ac.uk/intact/main.xhtml        (推荐)

 

BIND--The Biomolecular Interaction Network Database. PMID: 11125103  http://binddb.org

 

The MIPS mammalian protein-protein interaction database. PMID: 15531608 http://www.helmholtz-muenchen.de/en/ibis (http://mips.helmholtz-muenchen.de/proj/ppi/)

 

MINT: the Molecular INTeraction database. http://mint.bio.uniroma2.it/mint/

 

REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Pathway annotations are authored by expert biologists, in collaboration with Reactome editorial staff and cross-referenced to many bioinformatics databases. These include NCBI Entrez Gene, Ensembl and UniProt databases, the UCSC and HapMap Genome Browsers, the KEGG Compound and ChEBI small molecule databases, PubMed, and Gene Ontology. ... [more]

 http://www.reactome.org/ (推荐)

植物(reactome的子集)

http://n55960.nbi.bbsrc.ac.uk/download/all_interactions.html

BioGRID is an online interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.1.72 and searches 24,876 publications for 365,574 raw protein and genetic interactions from major model organism species. All interaction data are freely provided through our search index and available via download in a wide variety of standardized formats

http://www.thebiogrid.org/ (推荐)


Protein Interaction Analysis
Experimental Interactions
Predicted Interactions
Others
Structure 3-D
Small Molecules & Peptides
Interactions Nucleic Acid - Proteins
Software
All Links on Protein Interactions

Experimental Interactions
MIPS
The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions.
http://mips.gsf.de/proj/ppi/
BIND
Biomolecular INteraction Network Database
http://bond.unleashedinformatics.com/Action?
IntAct
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
http://www.ebi.ac.uk/intact/site/index.jsf
DIP
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
http://dip.mbi.ucla.edu/
MINT
Molecular INTeraction database. MINT focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the 'MINT Viewer'.
http://mint.bio.uniroma2.it/mint/Welcome.do
HomoMINT
Homomint is a web available tool extending protein-protein interactions experimentally verified in models organisms, to the orthologous proteins in Homo sapiens.
http://mint.bio.uniroma2.it/HomoMINT/Welcome.do
BioGRID
The Biological General Repository for Interaction Datasets (BioGRID) database was developed to house and distribute collections of protein and genetic interactions from major model organism species. BioGRID currently contains over 198 000 interactions from six different species, as derived from both high-throughput studies and conventional focused studies.
http://www.thebiogrid.org/
HPRD
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/
APID
APID (Agile Protein Interaction DataAnalyzer) is an interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a common and comparative platform.
http://bioinfow.dep.usal.es/apid/index.htm

Predicted Interactions
String
STRING is database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations.
http://string.embl.de//
InterPreTS
Interaction Prediction through Tertiary Structure web-based tool to predict protein-protein interactions.
http://www.russell.embl.de/cgi-bin/interprets2
I2D
I2D ( Interologous Interaction Database) is designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks.
http://ophid.utoronto.ca/ophidv2.201/ppi.jsp
SPPIDER
Solvent accessibility based Protein-Protein Interface iDEntification and Recognition
http://sppider.cchmc.org

Others
PPI
Protein-Protein Interaction Web site at the Jena Center for Bioinformatics
http://www.imb-jena.de/jcb/ppi/
CYGP
PPI section of the Comprehensive Yeast Genome Database.
http://mips.gsf.de/proj/yeast/CYGD/interaction/
HIV PI Database
Interactions between HIV and host proteins at the NCBI
http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/
ICBS
A database of protein-protein interactions mediated by interchain ?-sheet formation
http://www.igb.uci.edu/servers/icbs/
HPID
Human Protein Interaction Database at Inha University.
http://wilab.inha.ac.kr/hpid/
HUGE-PPI
A database of protein-protein interactions between large proteins
http://www.kazusa.or.jp/huge/ppi/
UniHI
Search the Unified Human Interactome
http://theoderich.fb3.mdc-berlin.de:8080/unihi/?

Structure 3-D
3DID
The database of 3D Interaction Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known.
http://gatealoy.pcb.ub.es/3did/
SNAPPI
SNAPPI stands for Structures, iNterfaces and Alignments for Protein-Protein Interactions. The SNAPPI-Package consists of SNAPPI-DB, SNAPPI-View and SNAPPI-Predict.
http://www.compbio.dundee.ac.uk/SNAPPI/index.jsp
Protcom
This database is a collection of protein-protein homo- and hetero-complexes as well as domain-domain structures.
http://www.ces.clemson.edu/compbio/protcom/

Small Molecules & Peptides
Domino
DOMINO: a database of domain-peptide interactions. Many protein interactions are mediated by small protein modules binding to short linear peptides. DOMINO is an open-access database comprising more than 3900 annotated experiments describing interactions mediated by protein-interaction domains.
http://mint.bio.uniroma2.it/domino/
JenPep
JenPep is a database of quantitative binding data for immunological protein-peptide interactions.
http://www.jenner.ac.uk/JenPep/
PDZBase
PDZBase is a manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains.
http://icb.med.cornell.edu/services/pdz/start
BindingDB
BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.
http://www.bindingdb.org/bind/index.jsp
iSPOT
SPOT (Sequence Prediction Of Target) is a procedure that is designed to infer the peptide binding specificity of any member of a family of protein binding domains: SH3, PDZ, and WW domains.
http://cbm.bio.uniroma2.it/ispot/

Interactions Nucleic Acid - Proteins
BindN
BindN for prediction of DNA and RNA binding residues in proteins
http://bioinfo.ggc.org/bindn/
DP-Bind
Web server for sequence-based prediction of DNA-binding residues in DNA-binding proteins.
http://lcg.rit.albany.edu/dp-bind/
DBS-PRED
This program predicts the DNA-binding in a protein from their sequence information using neural network.
http://gibk26.bse.kyutech.ac.jp/jouhou/shandar/netasa/dbs-pred/
ProNIT
ProNIT database provides experimentally determined thermodynamic interaction data between proteins and nucleic acids.
http://gibk26.bse.kyutech.ac.jp/jouhou/pronit/pronit.html
Protein-Nucleic Acid Recognition
Various tools and databases on DNA-protein recognition.
http://gibk26.bse.kyutech.ac.jp/jouhou/3dinsight/recognition.html

Software
Osprey
Software platform for the visualization of complex interation networks.
http://biodata.mshri.on.ca/osprey/servlet/Index
visANT
An integrative platform for network/pathway analysis; visANT = Integrative Visual Analysis Tool for Biological Networks and Pathways.
http://visant.bu.edu/

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