Everyone, SMILES!

OK, so today we're going to learn about Simplified molecular-input line-entry system, but since this title is already too long and I'm afraid you won't read any further dreading how long the post will be. So here's the good news. We're changing the title to SMILES. Short, simple, and sort of...fun. I guess.

But unfortunately, we're not smiling to each other here. Of course the main reason is I will never now if you actually will smile, but actually:

“SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings”.

In other words, it’s the way we type the notation of chemical molecules using a this SMILES system. Since it’s in ASCII strings, it can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. Convenience isn’t? This system is very widely used by academician worldwide.

Let’s see two types of SMILES:

Canonical SMILES	Isomeric SMILES
version that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation	version that includes extensions to support the specification of isotopes, chirality, and configuration about double bonds

Few characteristics:

l We use certain letters to represent atoms

l Hydrogens are removed, and cycles ane broken

l Numeric suffix used between broken cycles

l Parentheses used to indicate branching in the molecule tree

And these are the symbol for bonds...

Single bond	-
Double bonds	=
Triple bonds	#
Aromatic	*omitted

SMILES Charges

Specify attached hydrogens and charges in square brackets

Number of attached hydrogens is the symbol H followed by optional digit.

Further Restrictions

A branch cannot begin a SMILES notation - A branch cannot immediately follow a double- or triple-bond symbol-Example: C=(CC)C is invalid, butlC(=CC)C or C(CC)=C are valid SMILES

 

Disconnected Structures

Tetramethyl ammonium bromide  C[N+]C(C)C.[Br-]

Isomeric and Chiral SMILES

 l. Isomeric configuration indicated by forward and backward slashes: /  \

2. Examples:

–trans-1,2-dibromoethene: Br/C=C/Br

–cis-1,2-dibromoethene: Br/C=C\Br

3. Chirality indicated by the “@” symbol

Take a look at some examples

Well how was that? Enough? You can see more here  SMILESCAS Database

CHEMSKETCH KOI !!!

Assalammualaikum warahmatullahhi wabarakatuh...!!!!!!!!


All praises be to ALLAH the Almighty for He has blessed us 

with many favours, today we wanna share with all of you 

about the chemsketch..:) 





A commonly used chemical drawing program for 2D and 3D structures, 
copyright of Advanced Chemistry Development, Inc. The program has certain additional features including calculation of molecular weight, calculation of percentages of elements present, IUPAC name generation, and viewing in RasMol.

ACD/ChemSketch Freeware is a drawing package that allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logP.

Read more: http://www.answers.com/topic/chemsketch#ixzz2jHRdbFH7



Wait!!!
Before that...
to do the this chemsketch,once you must have the software.This software will help and guide you to create and build the chemsketch correctly...

Here i would like to share with you guys the link to download the chemsketch software.

--->click below to get the new software for chemsketch:
                                                 
                                                   chemsketch freeware download 



The freeware version of ChemSketch does not include all of the functionality of the commercial version.
Otherwise,you can visit to this link to learn more about commercial version:


click--->complete software package for drawing chemical structures.




Once you had download the software. You must install into your computer manually..Just follow the step and wait until the software completely installed..
Then,there will outcome a dropbox..click chemsketch application..

                  \
                           The sample application will look like this..


Now you can happily sketching..

If you want to run ChemSketch under Windows 98 or older, or under Linux, see Notes: Requirements and versions.

                                             figure 1.1

 Screen shot of the upper left hand corner of the opening screen.
Two of the tool buttons are already "lit up" when you open ChemSketch. One of these is along the left side, labeled C, for carbon. The other is a tool that looks something like a pencil drawing a line, along the 2nd horizontal row of tools near the 20-25 tics on the ruler. This tool, named "Draw Normal", is the tool you use for ordinary drawing.
Also, ChemSketch is in "structure" mode, as indicated by the word "Structure" being lit up (upper row of buttons, at left).
All of the settings mentioned here should be ok when you first open ChemSketch. However, if you change them, you may need to get back to them.

                                                                      figure 1.2

Screen shot of the lower left hand corner of the ChemSketch screen-- after the 3D Viewer has been opened.
Note the "Copy to 3D" and "3D View" buttons, above/right of the Start button (which is shown in its default, most common, location at the lower left of the screen), and three lines below the default palette. (Also note the button there labeled "ChemSketch". When you are in the 3D module, this button at the lower left, near Start, lets you switch back to the ChemSketch module.)




Otherwise....here also i would like to share with you guys the sample of exercise that my friend and i have done before..huhu

This is sketching of lipid

                                                               This is sketching of DNA

Tis is sketching of type of orbital.

                            This is sketching of multiple apparatus

FEATURES OF CHEMSKETCH	BENEFIT
Draw reactions and reaction schemes, and calculate reactant quantities	Visualize chemical structures in 2D or 3D
Predict logP for individual structures	Create professional reports, structures, text, and graphics simultaneously
Generate structures from InChI and SMILES strings
Generate IUPAC systematic names for molecules of up to 50 atoms and 3 ring structures
Search for structures in dictionary of over 165,000 systematic, trivial, and trade names                                          T                                             A                                                B                                                    L                                                         E                                                             1

ComE anD LEaRn XML!!

Assalamualaikum... Hi there! So let's take a look at this post.
Do you know what is XML? People usually know what is HTML right? Then today I will briefly explained about XML. Spend your time for a while here :)

XML was designed to describe data and focus what data is. XML stand for Extensible Markup Language. It is like HTML but they are not the same things. Some differences that I recognize between his two languages are shown as follow in this table below.

TYPE	HTML	XML
Differences	Designed to display data,focus on how data looks	Designed to transport and store data,focus on what data is
	Display information	Carrying information
	Case insensitive	Case sensitive
	Does not preserve white space	Preserve white space

Now you can see the differences right? 

Then let us look into another point about XML. For your information, XML documents form a tree structure. It must contain root element and we call this element as a parent. The tree start at the root and branches to the lowest level of the tree. Besides, all element can have sub elements(child elements). Let me show you an example below : 

<root>
 <child>
 <subchild>...</subchild>
</child></root>

tree structure#1

tree structure#2
Fuh, XML is quite interesting right? :)
Some of there syntax rules of XML are:

a)all elements must have a closing tags

b)XML tags are case sensitive

c)XML elements must be properly nested

d)XML documents must have a root element

e)XML attributes values must be quoted

XML also have its own rules to name the elements. 

• can contain letters, numbers and other characters
• cannot start with a number or punctuation characters

To make you more understand about this, I kindly prefer some links that will explain more to you about this. Here I attach some interesting links for you. 

Naming rules

Naming rules#2

So, hows about it? Did you enjoy learning XML with me?
Feel free to visit this site for more information about XML.

Hey, come here and learn with me! What is XML??

That is from me. Hope you will get some ideas about XML now.
:)
May we meet again. Bye...

HTML

ASSALAMUALAIKUM :)

Today we had learn how to used the HTML code.We studied 3 types of HTML which were :

• how to make list
• how to make link
• how to put the images

 The are some basic way to use HTML. First we must put <html> and followed by  <body> on the top  as 

the header of the code and at the end of it, we must put </body> and followed by </html> as the ending of every coding. Note that we must put "/" when we want to closed the <xxxx>. As example, when we want to make a variable X, we must put <li>X</li>.
Then we go to the 1st type; making list.When we want to start to do list, we must have the title for the list then we should included the types of the list either bullets or letter list or so on. For example

<h4>Example title for bullet list<h4>
<Ul type="disc">
 <li>apples<li>
 <li>bananas</li>
 <li>lemons</li>
 <li>oren</li>
</ul>

The re are two type of list, ordered (written by 'oi') and disordered ('ui'),

the type is written in quote after the 'type='.

The result for these are shown below:

Example title for bullet list :

• apples
• bananas
• lemons
• oren. 

Second parts is about  making link. The only difference between link and to make list is we should have this code:

<a href= "http://google.com"> see also this link.</a>

Noticed that we add href and we must attach the link after the href. The title will appear before the </a>.

The last thing is about the image.The coding syntax to put the image into our webpage is  

<img src="Smiley.gif" alt="Smiley face" width="32" height="32" />

We must include the <img ... /> for an image.

After 'src=' is the the name for our image that has been saved into the same folder or internet link

After 'alt=' is the name of our image. Followed by the dimension of the image.

Protein Data Bank

 Protein Data Bank (PDB)

Data of biological molecular structure available to public, including protein nucleic acids and viruses.

The data are submitted by scientist around the world

Founded in 1971 by Brookhaven National Laboratory, New York.

Currently it holds 29,000 released structures

Introduction to 5 types of Protein

1. LexA

2. Trypsin

3. HtrA

4. Pepsin

5. Amylase

   We will show you the structure of the proteins in 3-D views. The images are generated using the software RasMol. 
   The different colours in the images show different groups exist in the structures
   

LexA

These are the 3-D images of the structure LexA

LexA in ribbon view

Stick and ball vie

Further Information:  Data at RCSB

Amylase 

This is the common  enzyme found in human saliva

These are the 3-D images of the structure Amylase

Ball & Stick view

Ribbon view

Further Information:  Data at RCSB

Pepsin

 These are the 3-D images of the structure Pepsin

Ball and Stick view

Ribbon view

Further Information: Data at RCSB

 Trypsin

 These are the 3-D images of the structure Trypsin

Ribbon view

Stick and ball view

Further Information:Data at RCSB

HtrA

These are the 3-D images of the structure HtrA

Stick and Ball view

Ribbon view

Further Information: Data at RCSB

The following table summarize the information about these proteins

<![if !supportTabStrip]> <![endif]> <body> <p> This page uses frames, but your browser doesn't support them.</p> </body>

Name	Molecule	Polymer	Length	Chain
LexA	Lexa Repressor	1	202	A,B
Amylase	Amylase	1	496	A
Trypsin	Cationic Trypsin	1	223	A
Pepsin	Pepsin	1	326	A
HtrA	Serine protease HTRA1	1	332	A

Our First In IIUM Kuantan~~

Bismillahirahmanirahim Alhamdulillah,with His Blessing,we have been given the opportunity to further our study in IIUM Kuantan campus. It is on 3 September that all of us started to begin our journey here in Kuantan.

The enormous gate awaited us upon arrival

After zohor prayer, we began our Taaruf Programme.We were given Taaruf kit that consist of t-shirt, bagpack, batik and files.

Red being our theme colour this year

The briefing continued until 'Asr prayer. After that we did some outdoor activities at the OCD Square. We played some games such as 'mickey mouse' and 'chain of ukhuwah'. 

 

OCD Square, where we ran and laugh

At night, we slept at he mosque to perform qiamullail together before dawn and hear a talk by a lecturer

Performing congregational prayer in Sultan Haji Ahmad Shah Mosque

Here is the summary of our activities for first day in IIUM Kuantan.

Time	Activity	Venue
0800 - 1200	Registration	Grand Hall
1200 - 1400	Preparation and prayer	SHAS  Mosque
1400 - 1700	Briefing Part 1	Grand Hall
1700 - 1900	Prayer and outdoor activities	SHAS  Mosque, OCD Square
1900 - 2100	Self-activities	SHAS  Mosque
2100 - 2300	Briefing Part 2	Grand Hall
2300 - 0600	Sleep, qiamullail	SHAS  Mosque