Common websites and databases for proteomics research

Common websites and databases for proteomics research

1. Protein databases

1.UniProt (The Universal Protein Resource)

Website: http://www.uniprot.org/

http://www.ebi.ac.uk/uniprot/

Overview: Created jointly by EBI, PIR and SIB, this resource provides detailed protein sequences and functional information, including descriptions, domains, post-translational modifications and sites, variation, secondary and tertiary structures, with links to sequence, 3D structure, 2D gel and protein family databases.

2.PIR(Protein Information Resource)

Website: http://pir.georgetown.edu/

Overview: The source describes timely, high-quality annotation resources including iProClass, PIRSF, PIR-PSD, PIR-NREF and UniPort, with cross-references to over 90 biological databases covering protein families, functions, networks, interactions and genomes.

3.BRENDA(enzyme database)

Website: http://www.brenda-enzymes.org

Overview: An enzyme database providing classifications, nomenclature, reactions, specificity, structure, cellular localization, extraction methods, literature, applications, engineering and associated diseases.

4.CORUM(collection of experimentally verified mammalian protein complexes)

Website: http://mips.gsf.de/genre/proj/corum/index.html

Overview: A mammalian protein complex database providing complex names, subunits, functions and related literature.

5.CyBase(cyclic protein database)

Website: http://research1t.imb.uq.edu.au/cybase

Overview: A cyclic protein database providing sequences and structures, with prediction services.

6.DB-PABP

Website: http://pabp.bcf.ku.edu/DB_PABP/

Overview: A polyanion-binding protein database. The source describes roles of these interactions in localization, transport and folding, and their relationship to neurodegenerative disease. It contains identified polyanion-binding proteins and cross-references to the NCBI protein database.

7.IUPHAR-DB

Website: http://www.iuphar-db.org

Overview: A G protein-coupled receptor and ion channel database providing genes, functions, structures, ligands, expression profiles, signaling mechanisms and diversity.

8.GLIDA

Website: http://pharminfo.pharm.kyoto-u.ac.jp/services/glida/

Overview: A G protein-coupled receptor–ligand database providing interactions, ligands, receptors, homologous receptor networks and conserved recognition regions to support drug discovery.

9.LOCATE

Website: http://locate.imb.uq.edu.au/

Overview: A mammalian protein subcellular localization database.

10.InterPro

Website: http://www.ebi.ac.uk/interpro/

Overview: An integrated protein database combining information from multiple resources on domains, families and functional sites.

11.OKCAM

Website: http://okcam.cbi.pku.edu.cn

Overview: A human cell adhesion molecule database.

2. Proteome databases

1.GELBANK

Website: http://gelbank.anl.gov

Overview: Provides genome-wide two-dimensional gel electrophoresis proteome maps for organisms with known genome information, searchable by relative molecular mass, isoelectric point and protein sequence.

2.SWISS-2DPAGE

Website: http://www.expasy.org/ch2d/

Overview: Provides 2D-PAGE reference maps for human, mouse, E. coli, budding yeast and Dictyostelium.

3.SysPIMP(Systematical Platform for Identifying Mutated Proteins)

Website: http://pimp.starflr.info/

Overview: A protein mutation database based on mass spectrometry; the source describes using changes in spectra from amino-acid substitutions to identify disease-associated mutations.

4.Sys-BodyFluid

Website: http://www.biosino.org/bodyfluid/

Overview: A human body-fluid proteomics database covering plasma/serum, urine, milk, tears, sweat, saliva, bone marrow fluid, cerebrospinal fluid and gastric fluid.

5.BloodExpress

Website: http://hscl.cimr.cam.ac.uk/bloodexpress/

Overview: A database of gene expression during mouse hematopoiesis.

6.CentrosomeDB(human centrosomal proteins database)

Website: http://centrosome.dacya.ucm.es

Overview: A human centrosomal protein database.

7.ConsensusPathDB

Website: http://cpdb.molgen.mpg.de

Overview: A human functional interaction network database with cross-references to other resources, covering protein interactions, biochemical reactions and gene regulation.

8.Proteome Analysis Database

Website: http://www.ebiac.uk.proteome/

Overview: A proteomics analysis database.

9.HPRD(Human Protein Reference Database)

Website: http://www.hprd.org/

Overview: A human protein literature database.

10.NOPdb

Website: http://www.lamondlab.com/NOPdb3.0/

Overview: A nucleolar proteome database.

11.EndoNet

Website: http://endonet.bioinf.med.uni-goettingen.de/

Overview: A cell communication network database providing hormone and hormone-receptor information.

3. Protein interaction and network databases

1.3DID(3D interacting domains)

Website: http://3did.irbbarcelona.org

http://gatealoy.pcb.ub.es/3did/

Overview: Collects interactions involving proteins with known 3D structures, searchable by domain, motif, sequence, GO code, PDB ID or Pfam code.

2.DOMINE

Website: http://domine.utdallas.edu

Overview: A domain interaction database.

3.PiSite(Database of Protein interaction sites)

Website: http://pisite.hgc.jp

Overview: Searches protein sequences for interaction sites using PDB-based information.

4.Binding MOAD

Website: http://www.BindingMOAD.org

Overview: Provides protein–ligand crystal structures, annotated ligands for proteins with known structures and experimentally measured affinity data.

5.Phospho.ELM

Website: http://phospho.elm.eu.org

Overview: A protein phosphorylation site database.

6.SuperSite

Website: http://bioinformatics.charite.de/supersite

Overview: A database of metabolite and drug binding sites in proteins, including binding and recognition mechanisms and conserved sites.

7.STITCH

Website: http://stitch.embl.de/

Overview: A protein–compound interaction network database.

8.Reactome

Website: http://www.reactome.org

Overview: A database of human pathways and processes, providing biochemical network diagrams, protein annotations and cross-references to resources including UniPort, KEGG and OMIM.

9.PID(Pathway Interaction Database)

Website: http://pid.nci.nih.gov

Overview: The source describes an NCI and Nature resource covering human cell signaling, regulation and cellular processes, searchable by molecule or metabolic process.

10.UniHI(Unified Human Interactome database)

Website: http://www.unihi.org

Overview: A human protein–protein interaction database searchable by protein name or metabolic pathway.

11.VirHostNet

Website: http://pbildb1.univ-lyon1.fr/virhostnet/index.php

Overview: A virus–host molecular interaction network providing protein interactions and associated annotations, searchable by gene, protein or pathway.

12.Bionemo(molecular information on biodegradation metabolism)

Website: http://bionemo.bioinfo.cnio.es

Overview: Collects proteins and genes associated with biodegradation, including protein sequences, domains and structures; gene sequences, regulatory elements and transcription units; and pathways and biochemical reactions.

13.PMAP

Website: http://www.proteolysis.org

Overview: A protein degradation pathway database.

4. Protein 3D structure databases

1.PDB(Protein Data Bank)

Website: http://www.rcsb.org/pdb

Overview: A biological macromolecular structure database providing 3D structures, sequence details and biochemical properties for proteins and nucleic acids.

2. SARST (Structural similarity search Aided by Ramachandran Sequential Transformation)

Website: http://sarst.life.nthu.edu.tw/

Overview: A database for efficient protein structure alignment.

5. Protein motif databases

1. CDD(Conserved Domain Database)

Website: http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml

Overview: The Conserved Domain Database (CDD) collects conserved-domain and protein sequence information. The source describes using CD-Search to identify conserved domains in protein sequences and help analyze or predict protein function.

2.Blocks

Website: http://blocks.fhcrc.org

Overview: A database for comparison of conserved regions in protein families.

3.CPDB(database of circular permutation in proteins)

Website: http://sarst.life.nthu.edu.tw/cpdb

Overview: A database of circular permutation (CP) motifs. CP can be viewed as joining the original N and C termini and creating new termini elsewhere. The source notes CP members in known protein families and describes CPSARST as a tool for searching for CP.

4.MegaMotifbase

Website: http://caps.ncbs.res.in/MegaMotifbase/index.html

Overview: A protein motif family and superfamily database providing 3D locations and torsion-angle information for known motifs.

5.Minimotif Miner

Website: http://mnm.engr.uconn.edu

Overview: A protein motif detection database offering motif searches in protein sequences.

6.Pfam

Website: http://www.sanger.ac.uk/Software/Pfam

Overview: Provides multiple sequence alignment and hidden Markov models of common protein domains.

6. Prediction databases

1.InterPreTS(Interaction Prediction through Tertiary Structure)

Website: http://www.russell.embl.de/cgi-bin/interprets2

Overview: Provides prediction of protein interactions from tertiary structures using the sequences of two proteins.

2.Predictome

Website: http://predictome.bu.edu

Overview: A database predicting functional relationships between proteins using three computational methods—chromosomal neighborhood, phylogenetic profiles and domain fusion—applied to 44 genomes.

7. Protein phosphorylation site databases

1.Phospho.ELM/PhosphoBase（http://phospho.elm.eu.org/）

2.PhosphoSite（http://www.phosphosite.org）

PhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation. See About PhosphoSite above for more informatio。