Biotech In My Heart

23 December, 2012

SMILING VS SMILES

Assalamulaikum.

Hello, how are you my friends?

Today, we want share with you about SMILES. Do you know what SMILES is about?

Maybe you think smiles is like this.

It is true.

But actually we want to tell you about Simplified Molecular Input Line Entry Specification (SMILES).

Simplified Molecular Input Line Entry Specification (SMILE) is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Its strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. For example in figure 1.

Visualization of 3-cyanoanisole as COc(c1)cccc1C#N.

Figure 1

It is simple, using atomic symbol and follows unique rules. It is used widely around the world computationally.

To write the molecules in SMILES you should follow symbol in the table bellow.

Symbol for SMILES

Single bond	-
Double bond	=
Triple bond	#
Aromatic *can be omitted	:
Branches	Atom enclosure in parentheses,( )
Atom in aromatic	Lower cases, example: c1ccccc1
[Fe++]	Iron(II) cation
Isomeric	/ or \. Example: trans-1,2-dibromoethene: Br/C=C/Br cis-1,2-dibromoethene: Br/C=C\Br
Chirality	@
Metal	[Al]

But there a certain rules we need to follow:

1. A branch cannot begin a SMILES notation

2. A branch cannot immediately follow a double- or triple-bond symbol

3. Numbers indicate start and stop of ring. Same number indicates start and end of the ring, entered immediately following the start/end atoms.

Do you want to try? You can click here

Introduction to XML

What is XML?

XML stands for EXtensible Markup Language
XML is a markup language much like HTML
XML was designed to carry data, not to display data
XML tags are not predefined. You must define your own tags
XML is designed to be self-descriptive

The Difference Between XML and HTML

XML is not a replacement for HTML.

XML and HTML were designed with different goals:

XML was designed to transport and store data, with focus on what data is
HTML was designed to display data, with focus on how data looks

HTML is about displaying information, while XML is about carrying information.

XML Does Not DO Anything

Maybe it is a little hard to understand, but XML does not DO anything. XML was created to structure, store, and transport information.

The following example is a note to Tove, from Jani, stored as XML:

<note>
<to>Tove</to>
<from>Jani</from>
<heading>Reminder</heading>
<body>Don't forget me this weekend!</body>
</note>

The note above is quite self descriptive. It has sender and receiver information, it also has a heading and a message body.

But still, this XML document does not DO anything. It is just information wrapped in tags. Someone must write a piece of software to send, receive or display it.

With XML You Invent Your Own Tags

The tags in the example above (like <to> and <from>) are not defined in any XML standard. These tags are "invented" by the author of the XML document.

That is because the XML language has no predefined tags.

The tags used in HTML are predefined. HTML documents can only use tags defined in the HTML standard (like <p>, <h1>, etc.).

XML allows the author to define his/her own tags and his/her own document structure.

XML is Not a Replacement for HTML

XML is a complement to HTML.

It is important to understand that XML is not a replacement for HTML. In most web applications, XML is used to transport data, while HTML is used to format and display the data.

My best description of XML is this:

XML is a software- and hardware-independent tool for carrying information.

XML is Everywhere

XML is now as important for the Web as HTML was to the foundation of the Web.

XML is the most common tool for data transmissions between all sorts of applications.

18 December, 2012

Chem Sketch is Amazing Software

Assalamualaikum wbr...

"Chem Sketch"...??

Truthfully, we never heard this term before until Dr Linda teach us about this awesome software. I think there is no software to sketch the chemical structure of compound but luckily it is exist.

First of all, the definition of Chem Sketch is an application that created to ease our work on the chemistry field, especially in Organic Chemistry.

There are so many functions that provide by the application. The most basic function is to sketch the molecular structures, most of it are skeleton type of molecular structures. We can also use it to generate SMILES and get information about molecules etc.

As what we learned on the class, we have to finish our task which is to draw the molecular structures. Even though the drawing is too complex, we succeed to finish and completed them by using Chem Sketch as shown below.

Figure 1

Figure 2

Figure 3

Figure 4

Figure 5

Figure 6

How amazing our drawing..?? Awesome right. Hehe Fortunately we have software which is Chem Sketch to help us sketch the structure beautifully.

After that, we had learned about the SMILES. This term is stand for 'Simplified Molecular Input Line Entry System'

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

SMILES strings can be imported most molecules editor for conversion back to two dimensional (2D) drawing or three dimensional (3D) model of the molecules.

Here the SMILES notation about the structure molecules we had drew above.

Molecules	S.M.I.L.E
Figure 1	OP(=O)(OC1C[C@H](O)O[C@@H]1COP(=O)(O)O)OC[C@H]2O[C@H](CC2O)N3C=C(C)C(=O)NC3=O
Figure 2	OP(=O)(OC1C[C@H](O)O[C@@H]1COP(=O)(O)O)OC[C@H]2O[C@H](CC2O)n4cnc3c4N=C(N)NC3=O
Figure 3	OP(=O)(OC1C[C@H](O)O[C@@H]1COP(=O)(O)O)OC[C@H]2O[C@H](CC2O)N3C=CC(N)=NC3=O
Figure 4	OP(=O)(OC1C[C@H](O)O[C@@H]1COP(=O)(O)O)OC[C@H]2O[C@H](CC2O)n4cnc3c(N)ncnc34
Figure 5	OP(=O)(OC1C[C@H](O)O[C@@H]1COP(=O)(O)O)OC[C@H]2O[C@@H](O)CC2O
Figure 6	O[C@@H]2[C@H](COC[C@@H]1OC(CO)[C@@H](O)C(O)[C@@H]1O)C(CO)O[C@@H](O)C2O