Assalamu'alaikum ....
For this post, we will share a brief information about ..
"PROTEIN DATA BANK"
Do you know what is PDB?...
It is actually a repository for 3-D biological macromolecular structure.
It includes proteins,nucleic acids and viruses. PDB is obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%) and all data are available to the public.This structure is actually submitted by biologists and biochemists from around the world.
PDB was founded in 1971 by Brookhaven National Laboratory, New York. The first set of data were entered on punched cards. Then with magnetic tapes.After that it is transferred to the Research Collaboratory for Structural Bioinformatics (RCSB) in 1998.Currently it holds 29,000 released structures.
PDB an important resource for research in the academic, pharmaceutical, and biotechnology sectors
Example:
- Will this molecule turns into a cancer cell?
- Can this combination of molecules cure common cold?
- How does radiation affect the RNA and DNA?
Protein Images
Structure of Squash Trypsin Inhibitor:
Structure of the Alpha Amylase
Structure of Phospholipase
Structure of clpp:
PDB data format
PDB data format is used to contain the coordinates and related information . In the late 1990’s macromolecular Crystallographic Information file (mmCIF) evolved. It conforms to well-documented standards and facilitates automated data management
Software Tools
There are various software tools can minimize the amount of manual labor
It helps scientists deposit their results quicker and also help validate their results
Commonly used software:
Data Query
| Search Fields | Example |
|---|---|
PDB ID
|
4HHB,2MHR
|
Contains Chain Type
|
Protein: IGNORE,Enzyme:YES
|
Citation Author
|
Stuart Taylor
|
Compound Information
|
Myoglobin
|
Number of chains
|
1-5
|
Structure Content
|
Present of Alpha
|
PDB Beta
Includes three tiers architecture: relational database, presentation
tier and an object-relational J2EE middle tier. It also a
dded XML as a file format
Uses freely distributed Java components:
- Lucene – Text indexing system
- JfreeChart – Charts generation
- Hibernate – Object/relational persistence
- Jboss – J2EE application server
Data Integration
Users are interested in enzymes, diseases and others beside macro molecular structure.
External data are included in PDB Beta
- Gene Ontology – Vocabularies of all known gene and protein
- Enzyme Commission – Repository of Enzymes
- KEGG Pathways – Molecule interaction networks
Data are collected and integrated weekly.
> Visit Protien Data Bank Website: RCHB Protein Data Bank
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