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