Protein Data Bank

This the 4th post for KOS course,
This is the other new thing that I have learned during my computer class...

We learn bout how to create a unique and colorful protein using RasMol. RasMol is a program for molecular graphics visualisation. You can download it from this website.

I tell you it was a 'bit" interesting even I am taking mathematics..hahaha! :)

Here are some information about protein data bank.

•  A repository for 3-D biological macromolecular structure 
• All data are available to the public 
• It includes proteins, nucleic acids and viruses 
• Obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%) 
• Submitted by biologists and biochemists from around the world  
 

You can go to Portal of Biological Macromolecular Structures to look out for more molecular structures.
I show you the protein picture of Crystal structure of a LexA protein from Thermotoga maritima that I created using RasMol sofware..have a look! (^_^)

You can also rotate, change the colour and change other settings of molecule structure. Here are the picures :

Example of Data query:

Search Fields	Example
PDB ID	4HHB, 2MHR
Deposition/Release Date	September 1 1996
Citation Author	S.S. Taylor
Contains Chain Type	Protein: Ignore, Enzyme: Yes, DNA
Compound Information	Myoglobin, Lysozyme
Number of Chains	1-5
Secondary Structure Content	Present of alpha min 80%

SMILES

Assalamualaikum,

The 3rd and the last post for my KOS 1110 class for today. 

SMILES... smiles here is not a facial expression but SMILES is actually something we learned in class. SMILES stands for Simplified Molecular Input Line Entry System. The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. Basically its a simplified way of writing  the notation for a chemical structure. The best way to see it is by looking at a few examples.

SMILES	Name	SMILES	Name
CC	ethane	[OH3+]	hydronium ion
O=C=O	carbon dioxide	[2H]O[2H]	deuterium oxide
C#N	hydrogen cyanide	[235U]	uranium-235
CCN(CC)CC	triethylamine	F/C=C/F	E-difluoroethene
CC(=O)O	acetic acid	F/C=C\F	Z-difluoroethene
C1CCCCC1	cyclohexane	N[C@@H](C)C(=O)O	L-alanine
c1ccccc1	benzene	N[C@H](C)C(=O)O	D-alanine

And here are the examples that I have been done at the class:

SMILE NOTATION

 SMILE NOTATION

This is were we can use Chemsketch. The program will generate the SMILES notation after we sketch the chmeical structure.

CHEMSKETCH

Assalamualaikum,

2nd post for my KOS 1110 class for today.  

CHEMSKETCH...

Unlike MAPLE, I think this program is a must for all students in a bio-related field (biomedicine, biotechnology etc). This program allows us to draw chemical structures, lab apparatus setups, DNA and many other graphics we might need to use in the future. We can draw an apparatus setup to prepare a lab manual or submit a lab report. We can draw chemical structures for class notes or for journal articles (if we plan on becoming an academician). It's quite simple to use once you learn how to.

These are the pictures that were generated by Chemsketch.
 

Furthermore, this program not only used by academician, it also used by another industry applications. Such as :

Applications
Academia
Accurate Property Predictions and Databasing of Chemical Knowledge: Reach Compliance
AgroChemical Research
Drug Discovery: Purity Assessment Using LC/MS
Environmental Chemistry
Flavors and Fragrance Research
Impurity Identification Using Technique-specific Tools

After all,  I think I prefer to learn Chemsketch more than Maple although I'm a Mathematics student. (^_^)...  If you want to try using this program, you can download the Chemsketch for free from this website, acdlabs. 

EXCEL

Assalamualaikum,

It's been awhile I haven't post anything for this blog, since we were busy with the KOS tutorial . And of course, here another KOS 1110 post. There'll be one more after this because we have to post out the result of our tutorial.So EXCEL I think most people are familiar with. Even the non-science students. EXCEL is a very helpful program which can be utilized for many things. Some of which include carrying out accounting/financial tasks, converting numerical scientific data into graphical displays and even help extrapolate experimental data.These are screen shots on how EXCEL can convert data in table form into graphs.

Here the data...

Temperature (in °C)	Percentage injured p
8	4.7
22	12.3
15	6.5
13	5.9

So, we just insert the data, respectively to their rows and column in the Excel.

And here the graph for the data...

We also need to make sure the line of the graph is matched with the result,so we just need to adjust the graph by using these tools...

To lookout for more information about Excel, we just search out in the internet or refer to here.

MAPLE

Assalamualaikum,

This is my 1st blog and my 1st post, this post is not a usual post. It's a special post for a subject I'm taking this semeter, Computers in Science. This post will be about a computer program that I have learned in the first half of the semeter, Maple.


Although I'm a Mathematical student , it was the first time I use the program. In my understanding, it is a program which we can use to solve and perform mathematical problems.

The general infomation about Maple that I got from the internet :

Maple is a general-purpose commercial computer algebra system. It was first developed in 1980 by the Symbolic Computation Group at the University of Waterloo in Waterloo, Ontario, Canada.
Since 1988, it has been developed and sold commercially by Waterloo Maple Inc. (also known as Maplesoft), a Canadian company also based in Waterloo, Ontario. The current major version is version 14 which was released in April 2010.

Maple is the essential technical computing software for today’s engineers, mathematicians, and scientists. Whether you need to do quick calculations, develop design sheets, teach fundamental concepts, or produce sophisticated high-fidelity simulation models, Maple’s world-leading computation engine offers the breadth and depth to handle every type of mathematics.

Examples of Maple code:

All the commands given to Maple are in the areas marked with >.
These are the input areas.
Press enter to execute the command.

> sample code;

The lines of code must end with either a semicolon or a colon. Note the difference between them:

> p - ln( p );

 

> p - ln (p ):

If the line of code ends with a semicolon, the order is validated and the software displays the answer in the output area. If the line of code ends with a colon, the order is validated, but the answer is not displayed.

Maple Features

Smart Document Environment
Math Equation Editor, Plot Annotations and Customizations, Visualization, Task Templates, MapleCloud Document Exchange, Slideshows, Interactive Assistants, Handwritten Symbol Recognition, Embedded Components: Buttons-Sliders-Dials and More, Context-Sensitive Menus, Exploration Assistant
Mathematics
Symbolic and Numeric Math,Comprehensive Mathematics,Linear Algebra,Units and Dimensions,Equation Solving,Tolerances

For overall, We learned how to use this program from the very basics, it took some time to familiarise with code that available in the program. After learning how to use the program for almost 2 months, I think it was a though program to handle. Some students may get stress during studying this program, because once you make a mistake, all the maple worksheet may affected, so you have to re-do the worksheet again. Nonetheless, it's always good to have learned at least the basics, so when there is a need to use this program, it will be more easier to do it.