Smiles Notation

Smiles is a good action that gives many benefit to our health. People looks very beautiful and more attractive when they are smiling.

hehehehehe......

but in this post, we are going to explain not that type of smile but the other type of "SMILES".

The words SMILES itself means Simplified Molecular Input Entry System. It is widely use AND computationally efficient. 

There are two types of SMILES:

1-Canonical SMILES

2-Isomeric SMILES

The term Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has single unique of SMILES representation.

The term Isomeric SMILES refers to the version of the SMILES specification that includes extensions to support the specification of isotopes, charity, and configuration about double bond

There are 4 types of SMILES bond:

Type	Smile Bond
SINGLE	-
DOUBLE	=
TRIPLE	#
AROMATIC	:

SMILES Symbols

The symbols are consist of string of alphanumeric characters and certain punctuation symbols for examples, B, C, N, O, P, S, F, Cl, Br, I.

These are some example of SMILES notation

SMILES notation

For any further information you can go to this website http://www.epa.gov/med/Prods_Pubs/smiles.htm

Learn about Extensible Markup Language(XML)..

Assalamualaikum to all readers..

This time we will explain to you a little bit about Extensible Markup Language(XML).

 XML was designed to describe data and focus what data is. XML also is a markup language much like HTML. For your information, XML is just a plain text and nothing special. Software that can handle plain text can also handle XML.The important thing you need to know about XML is that XML is NOT a replacement for HTML.
These are some advantages of XML:

• XML simplifes data sharing
• XML simplifies data transport
• XML makes your data more available
• XML is used to create new internet language

simple XML coding

From the "simple XML coding" the  <recipe> is the root element of the document and from the '<title>' until </preparation> are the child elements. Finally, the </recipe > defines the end of the documents. Root elements and child elements must be in the XML coding.

Maybe some of the readers curious about the differences between XML and HTML.
So, I will give you some of differences.

Types	XML	HTML
Goals	transport and store data, with focus on what data is	display data, with focus on how data looks
Function	carrying information	displaying information

Click here for more knowledge about XML ------> xml.tree.asp

I hope all of you enjoy read this brief explanation about XML. Goodluck!! 

Chemsketch

Hai. Today we can tell you about chemsketch.  What is Chemsketch?

Introduction :

Chemskecth is an Education Tool and we call this ACD or Chemsketch Freeware. That is allows you to :

• Draw and view structures in 2Dm or render in 3D to view from any angle.
• Draw reactions and reaction schemes, and calculate reactant quantities.
• Generate structures from InChl and SMILES strings.
• Generate IUPAC systematic names for molecules of up to 50 atoms and 3 ring structures.
• Predict logP for individual structures.
• Search for structures in the built-in dictionary of over 165,000 systematic, trivial, and trade names.
  
  Example images of Chemsketch Freeware :

For more information about Chemsketch, you can go to this website : http://www.acdlabs.com/products/draw_nom/draw/chemsketch/

Tutorial for the basic Chemsketch : http://www.youtube.com/watch?v=33lXOLW7JyU 

Name	Matric Number
Afiq Safwan Bin Dolah	1310827
Muhd Ruzaidi Bin Madda	1319663
Muhamad Maliki Bin Md Jusoh	1311937

Protein Data Bank..

Assalamualaikum W.B.T..We meet again in our new post which is about the Protein Data Bank(PDB).
Maybe some of you heard it(PDB) for a very first time and you don't have any idea about it. but it's okay because we will try to do our best to explain it to you.

First of all, do you know what is protein data bank? PDB is a respiratory for 3-D biological molecular structure.All the data are available to all user. there are 3 things in PDB which are proteins, nucleic acids and viruses. The data are obtained from x-ray crystallography or NMR spectroscopy. Protein Data Bank was founded in 1971 by Brookhaven National Laboratory, New York. PDB is one of the important resources for reseacher in the academic, biotechnology sectors and pharmaceutical.

Here we provide you some example of protein. Those protein are LexA, Htra, Trypsin, Pepsin and Amylase. we also give you the basic characteristic of these protein so that you can imagine how the proteins looks like. The unit of weight and length for these protein are in asymmetric unit.

Name : LexA
Weight : 44989.86
Length : 202
Chain : A,B
Classification : Hydrolase

Name : Trypsin
Weight : 29892.08
Length : 223
Chain : E
Classification : Complex(Proteinase/inhibitor)

Name : Htra
Weight : 14890.90
Length : 134
Chain : A
Classification : Protein binding

Name : Pepsin
Weight : 34591.93
Length: 326
Chain : A
Classification : Hydrolase

Name : Amylase
Weight : 48016.77
Length: 425
Chain : A
Classification : Alpha Amylase

       
     hopefully you can understand a little bit about Protein Data Bank(PDB) from our short explanation.we hope you can share this information with your friend because "sharing is caring".never forget that Allah gives knowledge to us to share with others not to hide it. So, if you want to know more about the PDB or the types of protein that exist in this world, you may go to the links below.

Types of Protein	Links
LexA	http://www.rcsb.org/pdb/explore/explore.do?structureId=1JHF
Trypsin	http://www.rcsb.org/pdb/explore/explore.do?structureId=2PTC
Htra	http://www.rcsb.org/pdb/explore/explore.do?structureId=2L97
Pepsin	http://www.rcsb.org/pdb/explore/explore.do?structureId=1YX9
Amylase	http://www.rcsb.org/pdb/explore/explore.do?structureId=1BAG