Bio-Trac 25 (Proteomics: Principles and Bio-Trac 25 (Proteomics: Principles and Methods) Methods) March 26 March 26 , 2004 , 2004 Zhang-Zhi Hu, M.D. Zhang-Zhi Hu, M.D. Senior Bioinformatics Scientist Senior Bioinformatics Scientist Protein Information Resource Protein Information Resource National Biomedical Research Foundation, National Biomedical Research Foundation, GUMC GUMC Tutorial: Tutorial: Bioinformatics Resources Bioinformatics Resources ( http://pir.georgetown.edu/~huz/class/bioin fo_resource.html )
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Bio-Trac 25 (Proteomics: Principles and Methods) March 26, 2004 Zhang-Zhi Hu, M.D. Senior Bioinformatics Scientist Protein Information Resource National.
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Bio-Trac 25 (Proteomics: Principles and Methods)Bio-Trac 25 (Proteomics: Principles and Methods)
NIH Biomedical Information Science and Technology NIH Biomedical Information Science and Technology Initiative (BISTI) Working Definition (2000)Initiative (BISTI) Working Definition (2000) - - Research, Research, development, or application of computational tools and development, or application of computational tools and approaches for expanding the use of biological, medical, approaches for expanding the use of biological, medical, behavioral or health behavioral or health datadata, including those to , including those to acquireacquire, , storestore,, organizeorganize, , archivearchive, analyze, or , analyze, or visualizevisualize such data. such data.
PubMed Literature DatabasePubMed Literature Database((http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Search&DB=PubMedhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=Search&DB=PubMed) )
Can you find which crystallin that has 3D structure determined using PIR text search?
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I. Sequence & Genomics DatabasesI. Sequence & Genomics Databases
GenBankGenBank: An annotated collection of all publicly available nucleotide An annotated collection of all publicly available nucleotide and protein sequences.and protein sequences.RefSeqRefSeq: NCBI : NCBI non-redundant set of reference sequences, including non-redundant set of reference sequences, including genomic DNA, transcript (RNA), and protein productsgenomic DNA, transcript (RNA), and protein productsUniProtUniProt Consortium DatabaseConsortium Database: : UUniversal protein knowledgebase, a niversal protein knowledgebase, a central resource of protein sequence and function from central resource of protein sequence and function from Swiss-ProtSwiss-Prot, , TrEMBLTrEMBL and and PIRPIR..LocusLinkLocusLink: Curated sequences and descriptions of genetic loci.: Curated sequences and descriptions of genetic loci.UniGeneUniGene: Unified clusters of ESTs and full-length mRNA sequences .: Unified clusters of ESTs and full-length mRNA sequences .OMIMOMIM:: Online Mendelian inheritance in man: a catalog of human Online Mendelian inheritance in man: a catalog of human genetic and genomic disorders.genetic and genomic disorders.Model Organism Genome DatabasesModel Organism Genome Databases:: MGD, RGD, SGD, Flybase…MGD, RGD, SGD, Flybase…
GeneCardsGeneCards:: Integrated database of human genes, maps, proteins and Integrated database of human genes, maps, proteins and diseases.diseases.SNP SNP Consortium DatabaseConsortium Database
II. Protein Family DatabasesII. Protein Family Databases
Whole Proteins PIRSF: A Network Classification System of Protein Families COG (Clusters of Orthologous Groups) of Complete Genomes ProtoNet: Automated Hierarchical Classification of Proteins
Protein Domains Pfam: Alignments and HMM Models of Protein Domains SMART: Protein Domain Families CDD: Conserved Domain Database
Protein Motifs PROSITE: Protein Patterns and Profiles BLOCKS: Protein Sequence Motifs and Alignments PRINTS: Protein Sequence Motifs and Signatures
III. Databases of Protein FunctionsIII. 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) WIT: Functional Curation and Metabolic Models BRENDA: Enzyme Database UM-BBD: Microbial Biocatalytic Reactions and Biodegradation Pathways
Cellular Regulation and Gene Networks EpoDB: Genes Expressed during Human Erythropoiesis BIND: Descriptions of interactions, molecular complexes and pathways DIP: Catalogs experimentally determined interactions between proteins 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)
Three GOs: Molecular Function Biological Process Cellular Component
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IV. Databases of Protein StructuresIV. Databases of Protein Structures
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 3D Structure PDB 3D Structure
(http://www.rcsb.org/pdb/)
Rat gamma-crystallin, Rat gamma-crystallin, chain A, B.chain A, B.
Can you do a text search Can you do a text search at PIR to find this?at PIR to find this?
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PDBsum:PDBsum:Summary and AnalysisSummary and Analysis (http://www.biochem.ucl.ac.uk/bsm/pdbsum)
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Protein Structural Classification (1)Protein Structural Classification (1)
CATH: Hierarchical domain classification of protein structures (http://www.biochem. ucl.ac.uk/bsm/cath_new/)
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=CRGE_RAT&job=2)
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VI. Proteomic ResourcesVI. Proteomic Resources
GELBANK (GELBANK (http://gelbank.anl.gov): 2D-gel patterns from completed ): 2D-gel patterns from completed genomes; SWISS-2DPAGE (genomes; SWISS-2DPAGE (http://www.expasy.org/ch2d/))
PEP: Predictions for Entire Proteomes: (PEP: Predictions for Entire Proteomes: (http://cubic.bioc.columbia.edu/ pep/): Summarized analyses of protein sequences): Summarized analyses of protein sequences Proteome BioKnowledge Library: (Proteome BioKnowledge Library: (http://www.proteome.com): Detailed ): Detailed information on human, mouse and rat proteomesinformation on human, mouse and rat proteomesProteome Analysis Database (http://www.ebi.ac.uk/proteome/): Online Proteome Analysis Database (http://www.ebi.ac.uk/proteome/): Online application of InterPro and CluSTr for the functional classification of application of InterPro and CluSTr for the functional classification of proteins in whole genomesproteins in whole genomesExpression Profiling databases: GNF (Expression Profiling databases: GNF (http://expression.gnf.org/cgi-bin/index.cgi, human and mouse , human and mouse transcriptome), SMD (transcriptome), SMD (http://genome-www5.stanford.edu/MicroArray/SMD/, Stanford , Stanford microarray data analysis), EBI Microarray Informatics (microarray data analysis), EBI Microarray Informatics (http://www.ebi.ac.uk/microarray/ index.html , , managing, storing and analyzing managing, storing and analyzing microarray datamicroarray data))