PDB rosmol

PROTEIN DATABASE

• it is the archive of experimentally determined three dimensional structure of biological macro molecules that serves a global community of researchers, educators and students. 
• the data obtained by X-ray crystallography or NMR spectroscopy and submitted by researchers to this website.
• the website is known as Protein Data Bank.
• it act as important resource for research in academic, pharmaceutical and biotechnology sectors.

 RASMOL

• it is computer program written for interactive molecular graphics visualization intended and used primarily for the depiction and exploration of biological macromolecules structures.
• it is used in Protein Data Bank 
• it reads in the 3-D coordinates for a molecule using pdf file format
• it allow one to rotate the molecule interactively

below are several type of enzymes with their structure and description.

 RENIN

Ketopiperazine-Based Renin Inhibitors: Optimization of the C Ring

CLASSIFICATION               : HYDROLASE
STRUCTURE WEIGHT         : 74547.03
MOLECULE                      : RENIN
POLYMER                        : 1
TYPE                               :  PROTEIN
LENGTH                          : 333
CHAINS                           : A, B
ORGANISM                      : HOMOSAPIEN

HTR A

HTR-like protein from Haloarcula marismortui

CLASSIFICATION               : TRANSFERASE
STRUCTURE WEIGHT         : 60054.17
MOLECULE                      : HTR A
POLYMER                        : 1
TYPE                               :  PROTEIN
LENGTH                           : 126
CHAINS                           : A, B, C, D
ORGANISM                      : HALOARCULA MARISMORTUI ATCC 43049

FRAGMENT PAS DOMAIN : RESIDUE 387 - 509

SUBTILISIN

What is the meaning of this things???Let's explore about that now...yeaayyyy...There are many types of subtilisin enzyme,but today we only focused on 4C3U subtilisin.

For 4C3U,the discription of this molecular can be summarise as follow:

CLASSIFICATION          : HYDROLASE
STRUCTURE WEIGHT     : 28911.24
MOLECULE                  : SUBTILISIN CARLSBERG
POLYMER                    : 1
TYPE                           : PROTEIN
LENGTH                      : 274

CHAINS                       : A

EC#                           : 3.4.21.62

ORGANISM                  : BACCILUS LICHENIFORMIS

DEGQ

Now,we proceed to the  next enzyme which is DegQ.We choose 3PV5 DegQ to describe in this blog.

The detail about enzyme 3PV5 can be summarise as follow :

CLASSIFICATION                 : HYDROLASE

STRUCTURE WEIGHT            : 191744.00

MOLECULE                         : DegQ

POLYMER                           : 1

TYPE                                  : PROTEIN

LENGTH                              : 451

MUTATION                           : N189G, P190G

ORGANISM                          : LEGIONELLA FALLONII

THERMOLYSIN

Our last enzyme for today is thermolysin 1KJO.Let's explore about this.

Same with previous structure,thermolysin 1KJO also have its own description. 

CLASSIFICATION              : HYDROLASE/HYDROLASE INHIBATOR

STRUCTURE WEIGHT        : 34876.02

MOLECULE                     : THERMOLYSIN

POLYMER                       : 1

TYPE                             : PROTEIN

LENGTH                         : 316

EC#                              : 3.4.24.27

ORGANISM                     : BACILLUS THERMOPROTEOLYTICUS

GENE NAME                    : NPR

Internet History & Growth

The internet refers to the global information system that is logically linked together by a globally unique address space based on Internet Protocol (IP). 

The history of the internet begins with the development of electronic computer in 1990s and the internet begans to take root out of a network developed by the Advanced Research Projects Agency (ARPA) to aid in the sharing of information and resources among researchers. 

The internet has given us the ability to connect with people from around the globe with a fews clicks of a button, making it easier than ever to keep in touch with our friends and family. Because of that, social networking is the biggest industry of our time, but it wasn’t always that way.

The Birth of Social Networking As We Know It

Geocities was among the first social networking sites on the internet, launching its website in 1994. Its intent was to allow users to create their own websites, dividing them into “cities” based on the website’s content. In 1995, TheGlobe.com was launched, offering users the ability to interact with people who held the same interests and publish their own content.

Two years later, in 1997, AOL Instant Messenger and SixDegrees.com were launched. This was the year instant messaging became popular and it was the first time internet users were able to create a profile and friend each other.

The New Millennium Brings the World Closer

Friendster was the pioneer of social networking. In it’s first three months, the social networking website acquired 3 million users, amounting to 1 in 126 internet users being members at the time.       Friendster served as the launching point for the widely popular MySpace, who cloned Friendster and launched after just 10 days of coding.

In the following years, other social networking websites like Classmates.com, LinkedIn and Tribe.net started to pop up, including what was to be the most popular social networking website in internet history.

Facebook.com was launched in 2004 with the intent to connect U.S. college students, starting with Harvard College. In it’s first month, over half of the 19,500 students signed up. After gaining popularity, Facebook opened it’s registration to non-college students, and in 2008, Facebook surpassed MySpace as the leading social networking website.

Social networking has come a long way since 1978, and we will all witness its evolution for years to come, forever changing the way people connect with one another.

smiles notation

Next, we will continue our lesson with smiles notation..... Do you know what is smile notation..?? Let's us discuss about it now..

What is smiles..???        

 

Smiles is a string obtained by printing the symbol nodes encountered in a depth-first tree travesal of a chemical graph. "Organic subset" of B, C, N, O, P, S, F, Cl, Br, and I, brackets can be omitted. Branches are described with parentheses, as in CCC(=O)O for pro.0pionic acid. Double and triple bond are represented by the symbols '=' and '#'. Ring closure labels are used to indicate connectivity between non-adjacent atoms in the SMILES.

SMILES BOND :)

SINGLE ----> -

DOUBLE ----> =

TRIPLE ----> #

AROMATIC ----> :

SMILES BRANCHES :)

CC(O)CC is 2-Butanol

OCC(C)C is iso-Butanol

OC(C)C is tert-Butanol

SMILES CHARGES :)

[H+] ..........PROTON

[OH-].......... HYDROXYL ANION

[OH3+].......... HYDRONIUM CATION

[Fe++]......... IRON(II) CATION

[NH4+].......... AMMONIUM CATION

X M L

xml 

Extensible Markup Languange

-   designated to describe data & focus what data is
-   created to structure,store & transport information
-   data will be available to all kind of reading machine
-   not a replacement but a complement for HTML
-   most common tool for data transmission between all sort of application

USAGE OF XML

• separates data from HTML
  *it will be easier if we concentrate using  HTML just for the layout & display, while for data we can store separately in XML files
• simplifies data sharing
  *data can be easily exchangeld between incompatible system, thus xml is known as one of most time-consuming and is greatly reduces the complexity since it can be read by different incompatible application
• simplifies platform changes
  *since data is  stored in text format, so it easier to upgrade it to new OS, new apps or new browser without losing data
• makes data more available
  *data can be available in all kinds of reading machines
• to create new Internet languange
  *exp ; XHTML is latest version of HTML
           ; RSS languange for news feeds

 

XML TREE
(not really like that! hehe)

 

THE REAL XML TREE

  

XML SYNTAX RULE

• all elementmust have closing tag
• tag are cASe SEnsiTiVe
  *exp : <incorrect>This is incorrect</Incorrect>
             <correct>This is correct</correct>
• must be properly nested
• must have root element(parent)
• attribute must be quoted
  *exp : <note date=12/11/2007>
             <note date="12/11/2007">
• comment must be in this format (<!comment>)
• white space is preserved

XML ELEMENTS

-Everything from elements start tag to elements end tag
-it may have attribute
-exp : 

<bookstore>
  <book category="CHILDREN">
    <title>Harry Potter</title>
    <author>J K. Rowling</author>
    <year>2005</year>
    <price>29.99</price>
  </book>
  <book category="WEB">
    <title>Learning XML</title>
    <author>Erik T. Ray</author>
    <year>2003</year>
    <price>39.95</price>
  </book>
</bookstore>

NAMING RULES!

1. CANNOT contain letters, numbers, other characters
2. CANNOT start with letters XML,xml,Xml,xML etc
3. CANNOT contain space 

 you might want further explaination about this, you may refer this :)

lastly, let us compare between XML and HTML

 

Difference between HTML and XML

XML	HTML
transport and store data	display data
focus on what data is	focus on how it look
carry information	display information

Hyper whatttt???

HyperTextMarkupLanguange also known as HTML.


WHAT THE ?????????????????????????????????

- it is the standard markup languange to create webpage
-written in form of HTML element that concists of tags enclosed in angle bracket, commonly comes in pair like  <h1> and </h1>  but there also unpaired and empty elements tags. (exp : <img>)
-each HTML represents different document file content
-it can be use to create list, table ,input image and create blog
 


HOW TO ??????????????????????????????????????

-MUST include several key components : tags, character-based data types, character references,
                                                                   entity references and document type declaration

• The DOCTYPE declaration defines the document type to be HTML
• 'The text between <html> and </html> describes an HTML document
• The text between <head> and </head> provides information about the document
• The text between <title> and </title> provides a title for the document
• The text between <body> and </body> describes the visible page content
• The text between <h1> and </h1> describes a heading
• The text between <p> and </p> describes paragraph

 CHALLENGE!

challenge yourself here. try to type these codes in your notepad and save as .html and test wether you can produce the same output like in the picture !

introduction

Example for simple coding

The output of the above code

LIST

 LINK

so how's your progress so far ?
here comes the last challenge to you ...................

IMAGE

 

so do you find this software interesting ?
to know more and detail knowledge about this software you can go to this link :)

and in order to make your tutorial more interesting , lets enjoy watching the tutorial here :)





that's all from us .
so we end our entry with a quote.

It is possible to fail in many ways...while to succeed is possible only in one way.

Aristotle (384 BC - 322 BC), Nichomachean Ethics

chemsketch for dummies !

Do you know what is the chemsketch ?

    It is a software that can be used to produce molecules, name of organic molecules as well as Lewis structure,  view as 3D models, stick models and space filling or ball are among other thing.

Here are some basic things to know about this software

Drawing your first ever molecule by chemsketch

TRY TO DRAW ETHANE !!

1. When you open this software, two of the tool buttons are already lit up. One is along the left side and labeled as C for carbon while the other one is a tool that looks like a pencil drawing a line named "Draw Normal".
2. As indicated by word "Structure", if it is lit up means that it is in structure mode and you now can draw your molecule.
3. By the single anywhere on your main screen, you can see CH₄ appear.
4.  Position the pointer over either C-region of that H₃C-CH₃. You will know when the pointer is properly positioned because a faint box will appear around the C atom you have chosen (along with its hydrogens). Single click.\
5. Tadaaaaa ! Now you should see a 2D structure of ethane. 

•  Here are some general information you might want to know.
  
  To add a Carbon, click on place where you want to add and use the C tool to operate it.
  Each time you add a C, the number of Hydrogen shown will adjust approriately.
  With this simple tools, you are drawing molecules of C and H.

To make things more interesting, lets move to the higher level and lets draw a complex structure.

For not letting this tutorial become a boring tools, let watch some beneficial video.

 

so now your level had been upgraded !

 How to name the structure?

click tool at title bar then choose Generates name for structure

 then you can have the name for your structure. 

*for you whose already in higher level and need more information or specific details, you might want to download the book HERE

so now you have some basic on Chemsketch and you are no longer a dummies! :)

BYEEEEEEEE

MAPLE SOFTWARE

What is Maple.......????????? Do you know about it guys? Today we will share with you about maple software.

For your information, maple is a powerful mathematical software packgae. It can be used to obtain both symbolic and numerical solution of problems in arithmethic,algebra,and calculus and to generate plots of the solution it generates.

Actually did you know how to have maple in you computer?For sure you have to download it first.

Here we will share with you the steps to install it.

First of all,click on the URL (link) for the file on the page. Your browser should give you the option either to open or save the file. Choosing "open" should cause the Maple software on the computer to start and the file will be loaded into Maple. Choosing "save" will give you a chance to save the file somewhere so you can open it later.If this approach doesn't work, try the following
Hold the mouse over the link on the page. The URL should point to a file in the form *.mw (or *.mws, or *.ms).

1. Right-click on the link. A menu will appear.
2. Select the Save Link As option. A "Save As" dialogue box will appear. You can then save the file (make sure it's a Maple -- *.mws -- file) on the computer.

Now,after the first step you will have maple in you computer~~

To start Maple, click (or doubleclick) on the Maple icon -- or click on Maple in the list of programs on your computer.

1. The Maple prompt looks like this: >
   In Maple, the user types in commands at the prompt. After typing Enter, Maple will display any relevant output and then a new prompt will appear.Note that typing Enter on a Windows computer means using either the regular Enter key on the keyboard or the Enter key on the number pad. However, on a Macintosh, the key on the keyboard is a Return key, not an Enter key.On a Macintosh,you must use the Enter key on the number pad for maple to process a command.
   
2. There are two different ways to type things into a Maple worksheet: text and input. Input is typed at the prompt. Text is information that is not actually processed by Maple. It is usually used for comments. To add text, you can turn a prompt into a text field. With the cursor at the prompt, click on the "T" button at the top of the window (or press Ctrl-T).If you are in a text field and you want to return to the prompt, you can click on the button next to the "T" button that looks like a Maple prompt (or press Ctrl-J). The button that looks like a summation sign next the the "T" can be used to insert (non-executable) mathematical notation into your text.
3. There are two ways to end a Maple command: with a semicolon or with a colon. If the command does not have either a semicolon or a colon, then Maple will not process the information.
   
   1. If you end the command with a semicolon, the information will be processed and the output will be displayed.
   2. If you end the command with a colon, the information will be processed, but the output will not be displayed.
4. Basic arithmetic: + - * /
   These are the four basic arithmetic operations used by Maple.
5.  Some examples:> 52 + 9;
   
   61 > 42 * 357;
   
   14994 > (52 + 9) / (42 * 357);
   
   _61 
   14994
6. The command evalf will turn output into a decimal value:> evalf ( (52 + 9) / (42 * 357) );
   
   .004068293984
7. A few more built-in functions and what they mean in Maple:
   

   2 ^ 3;	23
   exp (7);	e7
   ln (9);	log e 9
   log (72);	log e 72 Note: both ln and log indicate log base e. log does not indicate base 10. To get log base 10 of 72 type log[10](72)
   abs (47);	| 47 |
   sqrt (4);	the square root of 4
   sin (Pi);	sin (3.14159...)
   cos (2*Pi);	cos (2*3.14159...)
   arcsin(1/2);	sin-1 (1/2) or arcsin (1/2)
   arccos(sqrt(3)/2);	cos-1 (sqrt(3)/2) or arccos (sqrt(3)/2)

   Some examples:
   > log (10^4);
   
   ln(10000) > sqrt (25);
   
   5 > sin (2*Pi);
   
   0 > abs (-17.3);
   
   17.3
8. Maple is more than just a calculator, though. It can use variables. In order to assign a value to a variable, use :=For instance;
   > a := 17;
   
   a := 17 > b := 3:
   > a + b;
   
   20
9. The := assignment can also be used to write expressions. The command subs can be used to substitute a value into an expression. In the following example, f is an expression.> f := x^2 - 2*x + 1;
   
   f := x² - 2x + 1 > subs (x=3, f);
   
   4
10. In addition to expressions, Maple can also create functions. These are similar to expressions, but they use different notation. We will turn the above expression f into a function named g.> g := x -> x^2 - 2*x + 1;
    
    g := x -> x² - 2x + 1 > g(3);
    
    4
11. Maple also has a plot function. To plot the expression f over the range x=-5 to x=5, this is what you would enter at the prompt:> plot (f, x=-5..5);
    In Versions 4 and 5, the plot will automatically appear on your worksheet. In Version 3 and on the Macintosh, it will appear in a separate window. You can then copy the image from the window and paste it into your worksheet. Copy and Paste can be found under the Edit menu on every version of Maple.
    To plot g instead of f, you would type: plot(g(x), x=-5..5);
    
12. Note: You need to have taken calculus to understand this section.
    To take the derivative of an expression or a function, use the command diff. To take the integral of an expression or a function, use the command int. Again, using f and g:> diff (f, x);
    
    2x - 2 > diff (g(x), x);
    
    2x - 2 > int (f, x);
    
    ¹/₃x³ - x² + x > int (g(x), x);
    
    ¹/₃x³ - x² + x
13. Maple knows several constants. However, Maple is case sensitive. So if you are using one of these constants, make sure that it is properly entered. The constants are used in place of a regular number. Here are some constants in Maple and their mathematical equivalents:

    Pi	3.141592654...
    I	the square root of -1

14. When you open a saved worksheet in Maple, you will see all of the input and output that was on the screen when the worksheet was saved. However, Maple does not "know" what input was entered when the worksheet was originally used. So there is a command called Execute Worksheet that will execute all of the input again in the order it appears on the screen. On Windows Versions 4 and 5, click on the Edit menu, highlight Execute, and select Worksheet. On Windows Version 3, click on the Format menu and select the Execute Worksheet command.

In addition,you can explore more about maple code by open the link below :

click here

click here