1. Group member
1.1. Siti Hawa Munira A12QB0058
1.2. Nurul Asyiekin A12QB0049
1.3. Nurul Atiqah A12QB0050
1.4. Siti Khairunnisa A12QB0060
2. Why it is useful?
2.1. BioLip
2.1.1. For examining the biological relevance of ligands
2.2. BRENDA
2.2.1. Provide data collection of enzymes
2.3. NextProt
2.3.1. Provide variety types of information on human protein
2.4. Protein Cluster
2.4.1. Provide collection of proteins from complete genome of prokaryotes, plasmid, viruses, organelles, protozoa and plant.
2.4.2. To know protein cluster
2.5. Interpro
2.5.1. Useful for functional analysis of protein sequences
2.5.2. Predict present of domain and important sign
2.6. PBD
2.6.1. For 3D prediction
2.7. D2P2
2.7.1. For predictions of disordered protein
2.8. ePros
2.8.1. Provide energy profiles of protein structure
2.9. Genome3D
2.9.1. Predict domain structure and 3D models for proteins and model genome
2.10. EBI ENZYME PORTAL
2.10.1. Provide information about enzymes
3. Descriptions
3.1. BioLip
3.1.1. semi-manually curated database for high-quality, biologically relevant ligand-protein binding interactions
3.1.2. the Protein Data Bank, with biological insights mined from literature and other specific databases
3.2. BRENDA
3.2.1. collection of enzymes functional data, which are classified according to Enzyme Commission list.
3.3. NextProt
3.3.1. New human protein-centric knowledge platform
3.4. Protein Cluster
3.4.1. Collection of related protein sequences consists of protein derieved from annotation of whole genomes, organelles and plasmids.
3.5. Interpro
3.5.1. Integrated resource of protein
3.6. PBD
3.6.1. Providing an information about the 3D structures of large biological molecules, including proteins and nucleic acids
3.7. D2P2
3.7.1. Making statistical comparisons of the various prediction methods freely available to the prediction community, as well as facilitating biological investigation of the disordered protein space.
3.8. ePros
3.8.1. Energy profiles of protein structure.
3.9. Genome3D
3.9.1. Domain structure predictions and 3D models for proteins and model genome.
3.10. EBI ENZYME PORTAL
3.10.1. Various kind of information about enzymes: small molecule chemistry, biochemical pathways and drug compounds.
4. Types of databases
4.1. BioLip
4.2. BRENDA
4.3. NextProt
4.4. Protein Cluster
4.5. Interpro
4.6. PBD
4.7. D2P2
4.8. ePros
4.9. Genome3D
4.10. EBI ENZYME PORTAL
5. Organisation of NAR & its major grouping (15 major groups)
5.1. 1. Nucleotide Sequence Databases
5.1.1. International Nucleotide Sequence Database Collaboration
5.1.1.1. Eg. DDBJ-DNA Data Bank of Japan
5.1.1.2. Eg. GenBank
5.1.1.3. Eg. NCBI Biosample/BioProject
5.1.1.4. Eg. The Sequence Read Archive (SRA)
5.1.2. Coding and non-coding DNA
5.1.2.1. Eg. MethDB
5.1.2.2. Eg. Plant repeat database
5.1.2.3. Eg. TranspoGene
5.1.3. Gene structure, introns, and exons, splice sites
5.1.3.1. Eg. GeneTrack
5.1.3.2. Eg. Spliceosome Database
5.1.4. Transcriptional regulator sites and transcription factors
5.1.4.1. Eg. QuadBase
5.1.4.2. Eg. TFClass
5.2. 2. RNA Sequence Databases
5.2.1. 16S and 23S Ribosomal RNA Mutation Database
5.2.2. 3D rRNA modification maps
5.2.3. 5S Ribosomal RNA Database
5.2.4. Database for Bacterial Group II Introns
5.2.5. HIV Sequence Database
5.2.6. Ribosomal Database Project (RDP-II)
5.2.7. RNA Modification Database
5.2.8. The Small Subunit rRNA Modification Database
5.3. 3. Protein Sequence Databases
5.3.1. General sequense databases
5.3.1.1. Eg. Patome
5.3.1.2. Eg. UniProt
5.3.2. Protein Properties
5.3.2.1. Eg. BindingDB
5.3.2.2. Eg. REFOLD
5.3.3. Protein localization and targeting
5.3.3.1. Eg. CentrosomeDB
5.3.3.2. Eg. PeroxisomeDB
5.3.4. Protein sequence motifs and active sites
5.3.4.1. Eg. eBLOCKS
5.3.4.2. Eg. PHOSIDA
5.3.5. Protein domain databases; protein classification
5.3.5.1. Eg. FunShift
5.3.5.2. Eg. OrthoDB
5.3.6. Databases of individual protein families
5.3.6.1. Eg. BACTIBASE
5.3.6.2. Eg. Histone Database
5.4. 4. Stucture Databases
5.4.1. Small molecules
5.4.1.1. Eg. ChemBank
5.4.1.2. Eg. DrugBank
5.4.1.3. Eg. SuperDrug
5.4.1.4. Eg. SuperToxic
5.4.2. Carbohydrates
5.4.2.1. Eg. GlycoMapsDB
5.4.2.2. Eg. MonosaccharidesBrowser
5.4.3. Nucleic acid structure
5.4.3.1. Eg. 3DNALandscapes
5.4.3.2. Eg. QuadBase
5.4.3.3. Eg. RNA FRABASE
5.4.4. Protein structure
5.4.4.1. Eg. DSDBASE
5.4.4.2. Eg. IDEAL
5.4.4.3. SitesBase
5.5. 5. Genomic Databases (non-vertebrate)
5.5.1. Taxonomy and identification
5.5.1.1. Eg. GeneTrees
5.5.1.2. Eg. MetaRef
5.5.2. General genomics databases
5.5.2.1. Eg. BacMap
5.5.2.2. Eg. GenoList
5.5.3. Prokaryotic genomic databases
5.5.3.1. Eg. AlterORF
5.5.3.2. Eg. MicroScope
5.5.4. Unicellular eukaryotes genome databases
5.5.4.1. Eg. Camparasite
5.5.4.2. Eg. TBestDB
5.5.5. Fungal genome databases
5.5.5.1. Eg. YeastNet
5.5.5.2. Eg. YEASTRACT
5.5.6. Invertebrate genome databases
5.5.6.1. Eg. NEMBASE
5.6. 6. Metabolic and Signaling Pathways
5.6.1. Prokaryotic genome databases
5.6.1.1. Eg. NMPDR- National Microbial pathogen Data Resource
5.6.2. Enzymes and enzymes nomenclature
5.6.2.1. Eg. FunTree
5.6.2.2. Eg. MultiTaskDB
5.6.3. Metabolic pathways
5.6.3.1. Eg. Bionemo
5.6.3.2. Eg. Reactom
5.6.4. Protein-protein interaction
5.6.4.1. Eg. EndoNet
5.6.4.2. Eg. GeneNet
5.6.4.3. Eg. VirusMINT
5.6.5. Signalling pathway
5.6.5.1. Eg. Networkin
5.6.5.2. Eg. SPIKE
5.7. 7. Human and Other Vertebrate Genomes
5.7.1. Model organisms, comparative genomics
5.7.1.1. Eg. Animal Genome Size Database
5.7.1.2. Eg. TreeFarm
5.7.2. Human genome databases, maps and viewers
5.7.2.1. Eg. GeneAnnot
5.7.2.2. Eg. GeneLoc
5.7.3. Human ORFs
5.7.3.1. Eg. GeneSpeed
5.7.3.2. Eg. PlasmID
5.7.3.3. Eg. PReMod
5.8. 8. Human Genes and Diseases
5.8.1. General human genetics databases
5.8.2. General polymorphism databases
5.8.3. Cancer gene databases
5.8.4. Gene-, system-, disease-specific databases
5.9. 9. Microarray Data and other Gene Expression Databases
5.9.1. Eg. CycleBase
5.9.2. Eg. Gene expression Barcode
5.9.3. Eg. GeneNote
5.10. 10. Proteomics Resources
5.10.1. Eg. 2D-PAGE
5.10.2. Eg. PeptideAtlas
5.11. 11. Other Molecular Biology Databases
5.11.1. Drugs and drug design
5.11.1.1. Eg. BacMet
5.11.1.2. Eg. SuperNatural
5.11.2. Molecular probes and primers
5.11.2.1. Human OligoGenome Resource
5.11.2.2. PrimerBank
5.11.2.3. probeBase
5.11.2.4. RTPrimerDB
5.11.3. Eg. BioModels
5.11.4. Eg. PubMed
5.12. 12. Organelle Databases
5.12.1. Mitochondrial genes and proteins
5.12.1.1. Eg. Human MtDB
5.12.1.2. Eg. MitoDrome
5.12.1.3. Eg. MitoGenesisDB
5.12.2. Eg. Organelle DB
5.12.3. Eg. Organellle genomes
5.12.4. Eg. Plant Organelle Databases
5.13. 13. Plant Databases
5.13.1. General plant databases
5.13.1.1. Eg. GeneFarm
5.13.1.2. Eg. MetaCrop
5.13.2. Arabidopsis thaliana
5.13.3. Rice
5.13.4. Other plants
5.13.5. Eg. Chloroplast Genenome Database
5.14. 14. Immunological Databases
5.14.1. Eg. AntigenDB
5.14.2. Eg.Epitome
5.14.3. Eg.Protegen
5.14.4. Eg. The Immune Epitope Database (IEDB)
5.15. 15. Cell Biology
5.15.1. Eg. CloneDB
5.15.2. Eg. ExoCarta
5.15.3. Eg. MethylomeDB
5.15.4. Eg. NCBI Bookshelf