SMILES :)

Assalamualaikum guys.. hopefully you smile and happy always..

let us smile together......

huh, why i asked you to smile and smile today? haha..
actually just want you to get the mood because today we will learn about SMILES.. But not smile in that picture ok..;)

SMILES is the short form of Simplified Molecular Input Line Entry System. This system uses atomic symbol and a set of intuitive rules. It also uses hydrogen-suppressed molecular graphs(HSMG). There are two types of smiles.

1) Canonical SMILES
2)Isomeric SMILES

Let us introduce you a few types of bonds of SMILES:

BOND
SINGLE	shows a single bond(-)
DOUBLE	shows a double bond(=)
TRIPLE	shows a triple bond
AROMATIC	can be omitted

There are a few SMILES charges that we need to know. There are:

[H+]       : proton

[OH-]     : hydroxyl anion

[OH3+]  : hydronium cation

[Fe++]    : iron(II) cation

[NH4+]   : ammonium cation


Please take note that the further Restrictions for SMILES are:
*A branch cannot begin a SMILES notation
*A branch cannot immediately follow a double-or triple-bond symbol
*Example: C=(CC)C is invalid, but
*C(=CC)C or C(CC)=C are valid SMILES


How to draw the structure given???
Let us learn together..:)
If we want to draw this structure for example, we just can draw it by using the chemsketch application.
1) Open the chemsketch application
2) Choose the shape that we want to use / draw
3) Put the atom that we want to put ( in this case, Cl).

Here is another product that we can get...

So, to be more improve, you can practice by your own..
Remember, practice makes perfect!! :)

journey to PDB

">Assalamualaikum....
Today, we have learned two chapters. One of them is Protein Data Bank (PDB).
PDB is defined as a repository for 3-D biological macromolecular structure. It is founded in 1971 by Brookhaven National Laboratory in New York.

PDB first set of data were entered on punched cards. In 1998, it has been transferred to the research Collaborators for Structural Bioinformatics (RCSB).Currently, it holds 29 000 released structures.

Besides that, PDB is an important resource for research in the academic, pharmaceutical, and biotechnology sectors.
Will the molecule turns into a cancer cell?
Can these combinations of molecules cure common cold?
How does radiation effect the RNA and DNA?
These are types of application that can being solved when we use PDB.

 

The structure table above shows the things that can be defined by PDB.

No.	Type of proteins
1	Htra
2	subtilisin
3	collagenes
4	aminopeptidase
5	carboxypeptidae

The most interesting part when we learned PDB is this software can shows to us the image of the protein in different and attractive ways.This is the first time we explore such a beautiful protein structure.
Here,we serves to you some examples of the protein structures.

 carboxypeptidase

 aminopeptidase

 collageness

subtilisin

htra

See!!!How wonderful these structures right??

We had use this link protein data bank(PDB)  in order to download this all the structures.
Hope u will enjoyed  this topics same like us....;)