Thursday, December 19, 2013

[PDB] Protein Data Bank

PDB

Hi!!!

Here are some of the information about PDB.

The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database.) The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, and RCSB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.
Example of the  pdb:

1) Amylase

 Image for amylase:

please refer to this link to get more information
click this link.

2)Trypsin

Image for trypsin;


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click this link

3) Pepsin

image for pepsin:

please refer to this link to get more information
click this link

4) HtrA

image for HtrA:


please refer to this link to get more information
click this link

5) Carboxypeptidase

image for carboxypeptidase:

please refer to this link to get more information
click this link.

SMILES

SMILE

Today, we learned about SMILE notation that can be used in chemsketch application. Below are the example of SMILE quotation and its molecular structure.


Picture of SMILE notation and its molecular structure

What is SMILE?

The simplified molecular-input line-entry system or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII STRINGS. SMILES strings can be imported by most molecule editors  for conversion back into two dimensional drawings of three dimensional models of the molecules. We draw our SMILES using a specific program name CHEMSKETCH.



Some examples of application on SMILES notations



SMILES Name SMILES Name
CCEthane[OH3]+ Hydronium ion
O=C=O Carbon Dioxide [2H]O[2H] Dueterium Oxide
C#N Hydrogen Cyanide [235U] Uranium-235
c1ccccc1 Benzene F/C=C\F Z-difloroethane

Summary

Simplified Molecular Input Line Entry System (SMILES) Widely used AND computationally efficient Uses atomic symbols and a set of intuitive rules Uses hydrogen-suppressed molecular graphs (HSMG)

SMILESCAS Database
The PowerPoint version on this note. (More Detailed)

Other Examples of SMILES notation and its Molecular structure