1 Bio-Trac 25 (Proteomics: Principles and Methods) Bio-Trac 25 (Proteomics: Principles and Methods) April 4, 2008 April 4, 2008 Zhang-Zhi Hu, M.D. Zhang-Zhi Hu, M.D. Research Associate Professor Research Associate Professor Protein Information Resource, Department of Protein Information Resource, Department of Biochemistry and Molecular & Cellular Biology Biochemistry and Molecular & Cellular Biology Georgetown University Medical Center Georgetown University Medical Center Tutorial: Bioinformatics Resources (http:// pir.georgetown.edu/pirwww/workshop/bioinfo_resource.html )
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1 Bio-Trac 25 (Proteomics: Principles and Methods) April 4, 2008 Zhang-Zhi Hu, M.D. Research Associate Professor Protein Information Resource, Department.
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Bio-Trac 25 (Proteomics: Principles and Methods)Bio-Trac 25 (Proteomics: Principles and Methods)
April 4, 2008April 4, 2008
Zhang-Zhi Hu, M.D. Zhang-Zhi Hu, M.D. Research Associate ProfessorResearch Associate ProfessorProtein Information Resource, Department of Protein Information Resource, Department of Biochemistry and Molecular & Cellular BiologyBiochemistry and Molecular & Cellular BiologyGeorgetown University Medical CenterGeorgetown University Medical Center
• NIH Biomedical Information Science and Technology Initiative (BISTI) Working Definition (2000) - Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.
• Whole Proteins– PIRSF: Nonoverlapping Classification of Full Length Proteins Based on
Evolutionary Relationship– COG (Clusters of Orthologous Groups) of Complete Genomes– PANTHER: Proteins Classified into Families/Subfamilies of Shared Function– ProtoNet: Automatic Hierarchical Classification of Proteins
• Protein Domains– Pfam: Alignments and HMM Models of Protein Domains– SMART: Protein Domain Identification and Annotation– CDD: Conserved Domain Database
• Protein Motifs– PROSITE: Protein Patterns and Profiles– BLOCKS: Protein Sequence Motifs and Alignments– PRINTS: Compendium of Protein Fingerprints (a group of conserved motifs)
III. Databases of Protein Functions• Metabolic Pathways, Enzymes, and Compounds
– Enzyme Classification: Classification and Nomenclature of Enzyme-Catalysed Reactions (EC-IUBMB)
– KEGG (Kyoto Encyclopedia of Genes and Genomes): Metabolic Pathways– LIGAND (at KEGG): Chemical Compounds, Reactions and Enzymes– EcoCyc: Encyclopedia of E. coli Genes and Metabolism– MetaCyc: Metabolic Encyclopedia (Metabolic Pathways)– BRENDA: Enzyme Database– UM-BBD: Microbial Biocatalytic Reactions and Biodegradation Pathways
• Inter-Molecular interactions and Regulatory Pathways– IntAct: Protein interaction data from literature and user submission– BIND: Descriptions of interactions, molecular complexes and pathways– DIP: Catalogs experimentally determined interactions between proteins – Reactome - A curated knowledgebase of biological pathways – BioCarta: Biological pathways of human and mouse– GO: Gene Ontology Consortium Database
KEGG is a suite of databases and associated software, integrating our current knowledge on molecular interaction networks, the information of genes and proteins, and of chemical compounds and reactions. (http://www.genome.ad.jp/kegg/kegg2.html)
Lab
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BioCyc: EcoCyc/MetaCyc Metabolic Pathways
The BioCyc Knowledge Library is a collection of Pathway/Genome Databases (http://biocyc.org/)
Reactome: http://www.reactome.org/ • Collaboration of CSHL, EBI and GO Consortium• Curated resource of core pathways and reactions in human biology• Authored by biological researchers of field experts• Cross-referenced with NCBI, Ensembl and UniProt, HapMap, KEGG…• Inferred orthologous events in 22 non-human species (mouse, rat…)
• Protein Structure– PDB: Structure Determined by X-ray Crystallography and NMR– PDBsum: Summaries and analyses of PDB structures – MMDB: NCBI’s database of 3D structures, part of NCBI Entrez– SWISS-MODEL Repository: Database of annotated protein 3D
models– ModBase: Annotated comparative protein structure models
• Structure Classification– CATH: Hierarchical Classification of Protein Domain Structures– SCOP: Familial and Structural Protein Relationships– FSSP: Protein Fold Classification Based on Structure--Structure
Alignment
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PDB: Experimental 3D Structure Repository
(http://www.rcsb.org/pdb/)
Rat gamma-Rat gamma-crystallin (chain A, crystallin (chain A, B.)B.)
Can you do a text search at PIR to find this (CRGE_RAT)?
A database of annotated three-dimensional A database of annotated three-dimensional comparative protein structure modelscomparative protein structure models (http://swissmodel.expasy.org/repository/smr.php?sptr_ac=CRBA1_MOUSE&job=2)
http://swissmodel.expasy.org/repository/
http://swissmodel.expasy.org/
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VI. Proteomic Resources• GELBANK (GELBANK (http://gelbank.anl.gov): 2D-gel patterns of species with ): 2D-gel patterns of species with
completed genomes. completed genomes. • SWISS-2DPAGESWISS-2DPAGE ( (http://www.expasy.org/ch2d/): index of 2D-gels): index of 2D-gels• PEP (PEP (http://cubic.bioc.columbia.edu/ pep/): Predictions for Entire ): Predictions for Entire
Proteomes: summarized analyses of protein sequences Proteomes: summarized analyses of protein sequences • Integr8 (Integr8 (http://www.ebi.ac.uk/integr8/): A browser for information ): A browser for information
relating to completed genomes and proteomes, based on data relating to completed genomes and proteomes, based on data contained in Genome Reviews and the UniProt proteome setscontained in Genome Reviews and the UniProt proteome sets
• GPMdb GPMdb ((http://gpmdb.thegpm.org/): Mass spec proteomics ): Mass spec proteomics DatabasesDatabases
• PeptideAtlas (http://www.peptideatlas.org/): compendium of PeptideAtlas (http://www.peptideatlas.org/): compendium of peptides identified in a large set of tandem mass spectrometry peptides identified in a large set of tandem mass spectrometry proteomic experimentsproteomic experiments
• HUPO (http://www.hupo.org/): Human Proteome Organization to HUPO (http://www.hupo.org/): Human Proteome Organization to foste international proteomics initiatives.foste international proteomics initiatives.
PRIDE: centralized, standards compliant, public data repository for proteomics data
http://www.ebi.ac.uk/pride/
HUPO Plasma
Proteome Project
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Protein Examples
• Rabbit alpha crystallin A (UniProtKB: CRYAA_RABIT/P02493)
• Delta crystallin II (Argininosuccinate lyase) (UniProtKB: ARLY2_ANAPL/P24058)
• Any additional proteins of your interest for search and retrieval
Lab:
I.I. Text search / Information retrievalText search / Information retrieval1. Literature search and text mining
– Finding synonyms (BioThesaurus)Finding synonyms (BioThesaurus)– Information extraction (e.g., protein phosphorylation sites)Information extraction (e.g., protein phosphorylation sites)
2. Find the sequence for the rabbit alpha crystallin A chain3. Find all alpha crystallin A chain classified in protein families4. Search crystallins that have active enzyme activities5. Find crystallins that have determined 3D structures
II.II. Database contents (reports)Database contents (reports)1.1. Sequence & genomics databases (UniProt)Sequence & genomics databases (UniProt)2.2. Protein family databases (PIRSF)Protein family databases (PIRSF)3.3. Database of protein functions (KEGG)Database of protein functions (KEGG)4.4. Databases of protein structures (PDB)Databases of protein structures (PDB)5.5. Proteomics databases (Swiss-2D)Proteomics databases (Swiss-2D)