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Sunday, 23 December 2012

SMILES

smile! :)

assalamualaikum

do you know what is SMILES is?

Today we will introduced you with SMILES or known as the simplified molecular input line entry specification. SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. The SMILES stings can be imported by most molecule editors for conversion back into two-dimensional drawing or three dimensional models of the molecules.

There are two types of SMILES bond:

Conical SMILES

Refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation.

Isomeric SMILES

Refers to the version of the SMILES specification that includes extensions to support the specification of isotopes, chirality and configuration about the double bond.

SMILES Bonds

Single*	-
Double	=
Triple	#
Aromatic	:

SMILES Charges : specify attached hydrogens and charges in square brackets, the number of attached hydrogens is the symbol H followed by optional digit. For example:

[H+] proton

[OH-] hydroxyl anion

[OH3+] hydronium cation

[Fe++] iron(III) cation

[NH4+] ammonium cation

There are also restrictions of using SMILES, such as :
1. a branch cannot begin a SMILES notation
2. a branch cannot immediately follow a double- or triple-bond symbol

for example: C=(CC)C is invalid
C(=CC)C or C(CC)=C is valid

If you want to view the examples of SMILES, here are a few molecules with their correct SMILES strings. CLICK HERE ;-)

Tuesday, 9 October 2012

Introduction to XML

Assalamualaikum. Hi everybody :-)
Last Wednesday, we learnt how to make XML syntax. XML stands for Extensible Markup Language.XML was created to structure, store and transport information.XML is different from HTML because XML is about carrying information whereas HTML is about displaying information.
The following example is a note to Elena from Stefan, stored as XML.

<note>
<to>Elena</to>
<from>Stefan</from>
<heading>Remember</heading>
<body>Don't forget me this weekend!</body>
</note>

XML in syntax form.

XML is now as important for the Web as HTML was to the foundation of the Web. It is the most common tool for data transmission between all sorts of application, and is becoming more and more popular in the area of storing and describing information. To learn how make XML,you can click here for the tutorial :-)

A 'Well Formed'XML document has correct XML syntax. The syntax rules are:

XML syntax	Description
XML documents	must have a root elements
XML elements	must have a closing tag
XML tags	are case sensitive
XML attribute values	must be in quoted
XML elements	must be properly nested

Introduction of HTML

Assalamualaikum!

Our 4th assignment for this week is Introduction of HTML.
Do you know what is HTML? HTML is language for describing web pages.

HTML stands for Hyper Text Markup Language
HTML is a markup languange
A markup language is a set of markup tags
The tags describe document content
HTML documents contain HTML tags and plain text
HTML documents are also called we pages

You just need a computer, an Internet browser and a word-processing program such as Microsoft's Notepad or WordPad or MAc's Simple Text to write HTML.

This is the simple example that we had learn

in class and its result in the web page.

You can learn how to make a website in HTML Tutorial video. Start off with a solid foundation by learning some of the basics of HTML. In this HTML tutorial you will learn how to make a simple webpages.

The tutorial starts off with definitions for HTML. It then goes on to demonstrate how you can use Microsoft Notepad to create your HTML file. It explains what HTML tags are and how to use some of the basic ones. This tutorial also shows how to display the HTML file in a web browser.

This is basic text sections.

<p>	defines paragraph
<align>	defines alignment
<abbr>	defines abbreviation
<dfn>	defines definition
<address>	defines contact information for the author/owner of a document
<blockquote>	defines long quotation

Wednesday, 26 September 2012

Protein Data Bank

Assalamualaikum, today we learn about Protein Data Bank (PDB) using RasWin software. It's quite complicated, but interesting. We can observe the structure of protein in 3D with different kind of display such as wireframe, backbone, ball&stick and etc. We can also customize the colour according to temperature, structure, shapely and etc.

The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as protein and nucleic acids. 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 a key resource in areas of structural biology, such as structural genomic.

Structure of form III crystals of bovine pancreatic trypsin inhibitor.

Authors	Wlodawer,A.
Classification	Proteinase Inhibitor (trypsin)
Compound	1 Polymer 1 Ligands

Crystal structure of PAS domain of HTR-like protein from Haloarcula marismortui.

Authors	Ocipiuk, J.
Classification	Transferase
Compound	1 Polymer 2 Ligands

Crystal Structure of P Domain from Norwalk Virus Strain Vietnam 026 in complex with disordered HBGA type Lex

Authors	Hansman, G.S
Classification	Viral protein
Compound	1 Polymer 2 Ligands

Crystal Structure of ATP-dependent Clp protease subunit P from Francisella tularensi.

Authors	Kim, Y.
Classification	Hydrolase
Compound	1 Polymer 5 Ligands

Crystal structure of ClpP in tetradecameric form from Staphylococcus aureus

Authors	Zhang, J.
Classification	Hydrolase
Compound	1 Polymer

Wednesday, 19 September 2012

Chemsketch :)

Assalamualaikum..Hi there :)

Today is our second class of Computer in Science at IIUM Kuantan. This course is compulsory to all Sciences students. In this subject, we learn how to draw chemical structures and graphical images using Chemsketch. Chemsketch is a scientific software.

Drawing The Energy of Reaction Diagram

Summarized steps to draw the energy diagram:

1. Drawing a curve

2. Modifying curve

3. Drawing the X and Y axes

Drawing different kinds of orbital

3 types of orbitals :

1. P orbital

2. D orbital

3. PI type orbital

Drawing lipids and micelles

This is the table of our tasks based on the syllabus :

9.2	Drawing the energy of reaction diagram
9.3	Drawing different kinds of orbitals
9.6	Drawing lipids and micelles

This is link for download the chemsketch software chemsketch software :-)

Wednesday, 12 September 2012

Our First Day in IIUM Kuantan

Assalamualaikum.. Hi everyone :)

Today,we will tell you about our new journey in IIUM Kuantan. We started our registration on 4th September 2012 and there are few photos that will tell you some of our story here (: