NAR Database Organisation and Amylase Specification according to NAR databases

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NAR Database Organisation and Amylase Specification according to NAR databases by Mind Map: NAR Database Organisation  and Amylase Specification according to NAR databases

1. HOW NUCLEIC ACID RESEARCH DATABASE (NAR) IS BEING ORGANIZED

1.1. Major database categories

1.1.1. Nucleotide sequence Database

1.1.1.1. GenBank

1.1.1.2. EMBL Data Library

1.1.2. RNA sequence databases

1.1.2.1. Ribosomal Database Project

1.1.2.2. 5S Ribosomal RNA Database

1.1.2.3. European rRNA database

1.1.2.4. Aptamer Database

1.1.3. Protein sequence databases

1.1.3.1. SWISS-PROT

1.1.3.2. PIR

1.1.3.3. PROSITE

1.1.3.4. Restriction Enzyme Database(REBASE)

1.1.4. Structure databases

1.1.4.1. RCSB Protein Data Bank(PDB),

1.1.4.2. BARD

1.1.5. Genomic databases (non vertebrates)

1.1.5.1. The Gene Indices

1.1.5.2. MGD - Mouse Genome Database

1.1.6. Organelle databases

1.1.6.1. Chloroplast Genome Database

1.1.6.2. Organelle genomes

1.1.6.3. Plant Organelles Database

1.1.6.4. FUGOID

1.1.7. Plant databases

1.1.7.1. Chloroplast Genome Database

1.1.8. Metabolic and Signalling databases

1.1.8.1. Protein-protein interactions

1.1.8.2. ChemProt

1.1.8.3. Signalling pathways

1.1.8.4. Metabolic pathways

1.1.9. Human Genes and Diseases

1.1.9.1. CancerResource

1.1.9.2. Protein Mutant Database

1.1.10. Proteomics Resources

1.1.10.1. Biodefense Proteomics Resource Center

1.1.10.2. 2D-PAGE

1.1.10.3. AAindex

1.1.11. Immunological databases

1.1.11.1. ALPSbase

1.1.11.2. AntigenDB

1.1.11.3. InnateDB

1.1.11.4. IPD-MHC

1.1.12. Cell Biology

1.1.12.1. cloneDB

1.1.12.2. DNAtraffic

1.1.13. Human and other Vertebrate Genomes

1.1.13.1. AgBase

1.1.13.2. Animal Genome Size Database

1.1.13.3. ENCODE Project at UCSC

1.1.13.4. GeneAnnot

1.1.13.5. AgBase

1.1.14. Molecular Biology database

1.1.14.1. BioModels

1.1.14.2. Cell Image Library

1.1.14.3. BioNumbers

1.1.15. Microarray Data and other Gene Expression database

1.2. Number Of Collection

1.2.1. In 20th annual Database issue

1.2.1.1. 176 articles included

1.2.1.2. 88 new online database

1.2.1.3. 77 update articles

1.2.2. 1512 online databases

1.2.2.1. sorted into 15 categories

1.2.2.1.1. 41 subcategoris

1.2.2.2. In April 1991

1.2.2.2.1. 18 articles

1.2.2.3. In May 1992

1.2.2.3.1. 19 articles

1.2.2.4. In July 1993

1.2.2.4.1. 24 articles

1.2.2.5. In Year 2012

1.2.2.5.1. Focused on Molecular Biology

1.2.2.6. In Year 2013

1.2.2.6.1. Focused on improving human health

1.2.2.7. In Year 2014

1.2.2.7.1. 58 new molecular biology databases

1.2.2.7.2. Recent updates to 123 databases

2. BRIEF DESCRIPTION ON SELECTED DATABASE

2.1. CATALYTIC SITE ATLAS (CSA)

2.1.1. A database which consists of information on enzyme active site and catalytic residue in enzyme of 3D structure

2.1.2. Two types of entry provided

2.1.2.1. Original hand annotated entry

2.1.2.2. Homologous entry

2.1.3. The design of the database is complex

2.1.4. Jmol viewer provide visualisation of active site of an enzyme

2.1.5. Require high knowledge to master

2.1.6. Exhibit date of database being updated

2.1.7. Able to contact developer for information clarification purpose

2.2. UNIVERSAL PROTEIN RESOURCE (UniProt)

2.2.1. Resources are stable and can be accessed freely

2.2.2. Collaboration with

2.2.2.1. European Bioinformatics Institute (EBI)

2.2.2.2. Protein Information Resource (PIR)

2.2.2.3. Swiss Institute of Bioinformatics (SIB)

2.2.3. Core activities include

2.2.3.1. Organising protein sequences by carrying out analysis using computers

2.2.4. Significant elemets are

2.2.4.1. UniProt Knowlwdgebase

2.2.4.2. UniProt Reference Clusters

2.2.4.3. UniProt Archive

2.2.4.4. UniProt Metagenomic and Environmental Sequences Databases

2.3. ENZYME PORTAL

2.3.1. Information on enzymes from multiple in-house resources addressing particular data classes such as

2.3.1.1. Protein sequences & structure

2.3.1.2. Reactions

2.3.1.3. Pathway

2.3.1.4. Small molecules

2.3.2. These data reside in separate databases makes information discovery cumbersome

2.3.3. Main goal

2.3.3.1. simplify this process for end users.

2.3.4. Coverage of a great variety of fields and scopes.

2.3.5. Free resource that summarizes publicly available information

2.3.6. Updated period

2.3.6.1. Every three weeks

2.3.7. provides a concise summary of information from

2.3.7.1. UniProt Knowledgebase

2.3.7.2. Protein Data Bank in Europe (PDBe)

2.3.7.3. Rhea, a database of enzyme-catalysed reactions

2.3.7.4. Reactome, a database of biochemical pathways

2.3.7.5. IntEnz, a resource with enzyme nomenclature information

2.3.7.6. ChEBI and ChEMBL , which contain information about small-molecule chemistry and bioactivity;

2.3.7.7. MACiE for highly detailed, curated information about reaction mechanisms

2.3.7.8. EFO , the Experimental Factor Ontology, a system for annotation of experiments from which the enzyme portal retrieves disease-related information, concretely from children of its ‘disease’ entry.

2.4. PROTEIN DATA BANK JAPAN (PDBj)

2.4.1. Design of the database is simple and user-friendly

2.4.2. A member of worldwide Protein Data Bank

2.4.3. Accepts and processes exprimental data from

2.4.3.1. Asia

2.4.3.2. Oceania

2.4.4. Collaboration with

2.4.4.1. Research Collaboratory for Structural Bioinformatics (RCSB)

2.4.4.2. Biological Magnetic Resonance Data Bank (BMRB) USA

2.4.4.3. Protein Data Bank Europe (PDB e)

2.4.5. Significant elements are

2.4.5.1. RESTful

2.4.5.1.1. used to access search results by using PDBj MINE

2.4.5.2. PDB mmCIF Exchange Dictionary

2.4.5.3. Sequence Navigator

2.4.5.4. Structure Navigator

2.4.5.5. GIRAF (ligand binding sites for molecular structures)

2.4.5.6. eF-seek

2.4.6. Core activities of database are

2.4.6.1. accept and maintain exprimentally obtained molecular structures

2.4.6.2. 3D and graphical structures

2.4.6.2.1. ligand binding residues

2.4.6.2.2. subunits

2.4.6.2.3. regions with specific sequences

2.4.7. Update Period

2.4.7.1. Every week

3. WHY IS THE DATABASES HELPFUL FOR AMYLASE

3.1. CATALYTIC SITE ATLAS

3.1.1. Can be filtered according into different classification

3.1.1.1. GENOME

3.1.1.1.1. Ensembls Genomes Genes

3.1.1.1.2. Ensembls Gene

3.1.1.1.3. PomBase

3.1.1.1.4. HGNC

3.1.1.2. NUCLEOTIDE SEQUENCE

3.1.1.2.1. Sequence

3.1.1.2.2. Non-coding

3.1.1.2.3. Assembly contig

3.1.1.2.4. Transcriptome Assembly contig

3.1.1.3. PROTEIN SEQUENCE

3.1.1.3.1. Uni ProtKB

3.1.1.3.2. JPO

3.1.1.3.3. PRIDE

3.1.1.3.4. KIPO

3.1.1.4. MACROMOLECULAR

3.1.1.4.1. ChemBL assay

3.1.1.4.2. PDbe

3.1.1.5. SMALL MOLECULES

3.1.1.5.1. ChemBL activity

3.1.1.5.2. ChemBL target

3.1.1.6. GENE EXPRESSION

3.1.1.6.1. Array express

3.1.1.7. MOLECULAR INTERACTION

3.1.1.7.1. InTact interactor

3.1.1.7.2. InTact experiments

3.1.1.8. REACTION, PATHWAY AND DISEASE

3.1.1.8.1. OMIM

3.1.1.8.2. Reactome

3.1.1.8.3. BioModels

3.1.1.9. PROTEIN FAMILIES

3.1.1.9.1. MEDLINE

3.1.1.9.2. Patents

3.1.1.10. ONTOLOGIES

3.1.1.10.1. BioSamples Group

3.1.1.10.2. Biosamples

3.2. UniProt

3.2.1. Consist high number of genome sequences of amylase for variable organisms

3.2.2. Enable us to search information in various forms

3.2.2.1. BLAST

3.2.2.2. Align

3.2.2.3. Retrieve

3.2.2.4. ID Mapping

3.2.3. Expansion of large scale proteomics along with structural genomics make the analysis process of amylase easier

3.2.4. Information customized into a few groups

3.2.4.1. Protein names

3.2.4.2. Gene names

3.2.4.3. Organism

3.2.4.4. Length of gene sequence

3.3. Enzyme Portal

3.3.1. Search filters

3.3.1.1. Species

3.3.1.2. Compound

3.3.1.3. Disease

3.3.2. Enzyme summary

3.3.2.1. Enzyme summary tab contains the description of :

3.3.2.1.1. Enzyme function

3.3.2.1.2. Classification in the EC hierarchy

3.3.2.1.3. Information about the protein sequence

3.3.2.1.4. Any synonyms

3.3.3. Protein 3D structure

3.3.3.1. Protein structure tab shows any experimental 3D models of the enzyme

3.3.3.2. Only basic information on the model is displayed

3.3.4. Reactions and pathways

3.3.4.1. Reactions and pathways tab shows the biochemical reactions catalysed by amylase

3.3.4.2. Only summarized information is shown

3.3.5. Small molecules

3.3.5.1. Small molecules tab includes any available information from UniProtKB about :

3.3.5.1.1. Cofactors

3.3.5.1.2. Activators

3.3.5.1.3. Drugs

3.3.5.1.4. Any bioactive compounds

3.3.6. Diseases

3.3.6.1. Disease tab lists any diseases that are related to the selected enzyme

3.3.7. Literature

3.3.7.1. Literature tablists bibliographic citations relevant to the enzyme.

3.4. Protein Data Bank Japan

3.4.1. Easy to obtain experimental method for amylase

3.4.1.1. Electron Microscopy

3.4.1.2. ADIT-NMR that utilize 3D graphic of amylase

3.4.2. Contain various species for easier amylase classification

3.4.2.1. Human

3.4.2.2. Animal

3.4.2.3. Insects

3.4.2.4. Bacteria

3.4.2.5. Plant associated organisms

3.4.3. Consists of many tools that focusing on amylase structure

3.4.3.1. ePROT

3.4.3.2. Yorodumi (a tool that can generate the 3D structure based from experimental data)

3.4.3.3. EM Microscopy structures for any amylase structure obtained from the EM microscope

3.4.3.4. SeSAW tool for generating amylase structure prediction

3.4.4. Split entries feature

3.4.4.1. Large molecules that associated to amylase are split in different entries for enhanced search results

3.4.4.2. Able to superimposed data from two database (EMDB-PDB hybrid data)

3.4.5. Focusing to microscope resolution

3.4.5.1. Quick access to find amylase structure that is according to our resolution choice

4. PREPARED BY: 1) HARLEEN KAUR D/O DARSHAN SINGH 2) RAHMATH NISHA BT OMAR 3) NUR FATIEN ATIQA BT MOHD JAMAL 4) NUR FAZLINI B T MOHAMAD 5) NUR HIDAYAH BT MOHD KUSAIRI