Understanding PDB Protein Data Bank

What is PDB?

• 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.
• PDB is an important resource for research in the academic, pharmaceutical, and biotechnology sectors.
• Examples :

               - Will this molecule turns into a cancer cell?

               - Can this combination of molecules cure common cold?

               -How does radiation affect the RNA and DNA?

 Looking at Structures

Looking at Structures is designed to help you get started with charting a path through this material, and help you avoid a few common pitfalls. These chapters are intertwined with one another. To begin, select a topic from the right menu, or select a topic from below:

• PDB Data
  The primary information stored in the PDB archive consists of coordinate files for biological molecules. These files list the atoms in each protein, and their 3D location in space. These files are available in several formats (PDB, mmCIF, XML). A typical PDB formatted file includes a large "header" section of text that summarizes the protein, citation information, and the details of the structure solution, followed by the sequence and a long list of the atoms and their coordinates. The archive also contains the experimental observations that are used to determine these atomic coordinates.
• Visualizing Structures
  While you can view PDB files directly using a text editor, it is often most useful to use a browsing or visualization program to look at them. Online tools, such as the ones on the RCSB PDB website, allow you to search and explore the information under the PDB header, including information on experimental methods and the chemistry and biology of the protein. Once you have found the PDB entries that you are interested in, you may usevisualization programs to allow you to read in the PDB file, display the protein structure on your computer, and create custom pictures of it. These programs also often include analysis tools that allow you to measure distances and bond angles, and identify interesting structural features.
• Reading Coordinate Files
  When you start exploring the structures in the PDB archive, you will need to know a few things about the coordinate files. In a typical entry, you will find a diverse mixture of biological molecules, small molecules, ions, and water. Often, you can use the names and chain IDs to help sort these out. In structures determined from crystallography, atoms are annotated with temperature factors that describe their vibration and occupancies that show if they are seen in several conformations. NMR structures often include several different models of the molecule.
• Potential Challenges
  You may run into several challenges as you explore the PDB archive. For example, many structures, particular those determined by crystallography, only include information about part of the functional biological assembly. Fortunately the PDB can help with this. Also, many PDB entries are missing portions of the molecule that were not observed in the experiment. These include structures that include only alpha carbon positions, structures with missing loops, structures of individual domains, or subunits from a larger molecule. In addition, most of the crystallographic structure entries do not have information on hydrogen atoms.

Classification	Descriptions	Image
Amylase	Molecule : Alpha-1,4-glucan-4-glucanohydrolase Polymer : 1 Type : Protein
Trypsin	Molecule : Beta-trypsin Polymer : 1 Type : Protein
Hydrolase(acid Proteinase)	Molecule : Pepsin Type : Protein Polymer : 1
Carboxypeptidase	Molecule : Human Protective Protein Polymer : 1 Type : Protein
HtrA	Molecule : Probable serine protease HTRA3 Polymer : 1 Type : Protein

You can search many more type of proteins on this PDB website. Have a blast :)

SMILE

 

Simplified molecular input line entry specification


SMILES (Simplified Molecular Input Line Entry System) is a chemical notation that allows a user to represent a chemical structure in a way that can be used by the computer. SMILES is an easily learned and flexible notation. The SMILES notation requires that you learn a handful of rules. You do not need to worry about ambiguous representations because the software will automatically reorder your entry into a unique SMILES string when necessary.

The term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also commonly used to refer to both a single SMILES string and a number of SMILES strings; the exact meaning is usually apparent from the context. The terms Canonical and Isomeric can lead to some confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive.

 

Its describing the structure of chemical molecules using short ASCII. Specification is to describe structure of chemical molecules using short ASCII strings. Its can be imported by most molecule editors for conversion back into two-dimensional  drawings or three-dimensional models of the molecules.

               

Single	-
Double	=
Triple	#
Aromatic	:

                                              table for smile bond.

conical smile	isomeric smile
•version of SMILE specification includes rules for ensuring that each distinct chemical molecule has a single unique SMILE represents	•refers to the version of the SMILE specification that includes extension to support the specification of isotope, charity.

       Its also have a SMILE Brances. it is represented by enclosured in parenthesis. it can be catogorised as nested or stacked.


  Examples of Smile Bond

Ethene	C=C
Chloroethene	CIC=C
1,1-Dichloroethene	CIC(CI)=C
cis-1,2-Dichloroethene	CIC(CI)=CCI
Trichloroethene	CIC(CI)=CCI
Perchloroethene	CIC(CI)=C(CI)CI

   
     Smile chargesis a specify attached hydrogens and charges in squared brackets and these is the examples.

[H+]	proton
[OH-]	hydroxyl anion
[OH3+]	hydronium cation
[Fe++]	iron(ii) cation
[NH4+]	ammonium cation

   

 Acyclic compound is a compound in which a series of atoms is connected to form a loop of a ring. To get more info cyclic compound, you can click  HERE for the information. 

The Internet History And Growth

What is Internet?
The Internet is a global system of interconnected computer networks that use the standard Internet protocol suite (TCP/IP) to serve several billion users worldwide. It is a network of networks that consists of millions of private, public, academic, business, and government networks, of local to global scope, that are linked by a broad array of electronic, wireless and optical networking technologies.

Where does the Internet come from?

Created by the US government’s Advanced Research Projects Agency (ARPA) in the 1960s, the ARPANet was originally used by academic and government institutions. TCP/IP, or Transmission Control Protocol/Internet Protocol, was introduced to the ARPANet in 1983, at which point the Internet as we know it came to be.

TCP/IP makes it possible for computers everywhere to share data.  Under TCP/IP, a file is broken into smaller parts called "packets". Each packet is given the IP (Internet Protocol) address of the computer it has to travel to. As the packet moves through the global network, it is "switched" by a number of servers and routers along the way towards its destination.

The IP address tells those servers which way to switch the packet. Each time the packet is switched, a "wrapper" is added to the packet – this way we can tell how many computers and which computer handled the file while it was in transit.

The packets do not necessarily travel together on the Internet. Packets from the same file may travel via different paths through different servers, but always towards the same destination.

Internet Timeline

What is domain name?

Domain names are used to identify one or more IP addresses. For example, the domain name microsoft.com represents about a dozen IP addresses. Domain names are used in URLs to identify particular Web pages. For example, in the URL http://www.pcwebopedia.com/index.html, the domain name is pcwebopedia.com.

Every domain name has a suffix that indicates which top level domain (TLD) it belongs to. There are only a limited number of such domains. For example:

Names	Entity	Notes
.aero	air-transport industry	Must verify eligibility for registration; only those in various categories of air-travel-related entities may register.
.com	commercial	This is an open TLD; any person or entity is permitted to register. Though originally intended for use by for-profit business entities, for a number of reasons it became the "main" TLD for domain names and is currently used by all types of entities including nonprofits, schools and private individuals. Domain name registrations may be challenged if the holder cannot prove an outside relation justifying reservation of the name, to prevent "squatting".
.biz	business	This is an open TLD; any person or entity is permitted to register; however, registrations may be challenged later if they are not held by commercial entities in accordance with the domain's charter. This TLD was created to provide relief for the wildly popular .com TLD
.net	network	This is an open TLD; any person or entity is permitted to register. Originally intended for use by domains pointing to a distributed network of computers, or "umbrella" sites that act as the portal to a set of smaller websites.

For more information click this link!

Extensible Markup Language (XML)

 Last post, we were discussing regarding HTML

Today were are going to teach you guys about XML or Extensible Markup Language.

What You Should Already Know

Before you continue you should have a basic understanding of the following:

• HTML previous post
• JavaScript

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
• XML is a W3C Recommendation

XML Does Not DO Anything

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.

Characteristics of XML

XML You Invent Your Own Tags
XML is Not a Replacement for HTML
XML is a W3C Recommendation
XML is Everywhere

some rules in doing XML

 

l  XML Syntax Rules

l  XML Tags are Case Sensitive

l  XML Elements Must be Properly Nested

l  XML Documents Must Have a Root Element

l  XML Attribute Values Must be Quoted

l  XML Elements are Extensible

XML documents can form a tree structure which is like this :

XML Documents Form a Tree Structure

 

bookstore  

book category	title lang	author	year	price
COOKING	Everyday Italian	Giada De Laurentiis	2005	30.00
CHILDREN	Harry Potter	J K. Rowling	2005	29.99
WEB	Learning XML	Erik T. Ray	2003	39.95

 

 

 

here some questions for you guys to test your knowledge ! quiz thank you.

 

 

HTML Tutorial

HyperText Markup Language (HTML) is the main markup language for creating web pages and other information that can be displayed in a web browser.

HTML is written in the form of HTML elements consisting of tags enclosed in angle brackets (like <html>), within the web page content. HTML tags most commonly come in pairs like <h1> and </h1>, although some tags represent empty elements and so are unpaired, for example <img>. The first tag in a pair is the start tag, and the second tag is the end tag (they are also called opening tags and closing tags). In between these tags web designers can add text, further tags, comments and other types of text-based content.

The purpose of a web browser is to read HTML documents and compose them into visible or audible web pages. The browser does not display the HTML tags, but uses the tags to interpret the content of the page.

HTML elements form the building blocks of all websites. HTML allows images and objects to be embedded and can be used to create interactive forms. It provides a means to create structured documents by denoting structural semantics for text such as headings, paragraphs, lists, links, quotes and other items. It can embed scripts written in languages such as JavaScript which affect the behavior of HTML web pages.

Web browsers can also refer to Cascading Style Sheets (CSS) to define the appearance and layout of text and other material. The W3C, maintainer of both the HTML and the CSS standards, encourages the use of CSS over explicit presentation HTML.

• HTML files are nothing more than simple text files, so to start writing in HTML, you need nothing more than a simple text editor.

• Notepad is a common text editor on Windows-based computers (usually found under the Programs > Accessories menu) and Mac OSX computers come bundled with TextEdit but any program that lets you fiddle with text will do.

• Now create a folder called “html” wherever you like to save files on your computer and save the file as “myfirstpage.html”.

• To look at HTML files, they don’t even need to be on the web. Open a web browser such as Chrome, Firefox, Safari or Internet Explorer and in the address bar, where you usually type web addresses, type in the location of the file you just saved (for example, “c:\html\myfirstpage.html”) and hit return. Alternatively, go to the File menu of the browser, select Open, and browse for the file. Pow. There it is. Your first web page. How exciting. And all it took was a few typed words.

•  <html> is the opening tag that kicks things off and tells the browser that everything between that and the</html> closing tag is an HTML document. The stuff between <body> and </body> is the main content of the document that will appear in the browser window.

Type of Tag	Notation
body tag	<body>
paragraph tag	<p>content</p>
heading tag	<h1>heading tag </h1>
italic tag	<i>italic tag</i>
bold tag	<b>bold tag </b>

Example 1 - Introduction

• <h1> - headings
• <p> - defines paragraph 

Example 2 - Link

• An anchor tag (a) is used to define a link, but you also need to add something to the anchor tag - the destination of the link.
• The destination of the link is defined in the href attribute of the tag. The link can be absolute, such as “http://www.htmldog.com”, or it can be relative to the current page.
• So if, for example, you had another file called “flyingmoss.html” in the same directory then the line of code would simply be <a href="flyingmoss.html">The miracle of moss in flight</a> or something like this.

Example 3 - List

•  <ol> - defines ordered 
•  <ul> - defines unordered 
•  <li> - defines list item

Example 4 - Table

• The table element defines the table.
• The tr element defines a table row.
• The td element defines a data cell. These must be enclosed in tr tags, as shown above.
• If you imagine a 3x4 table, which is 12 cells, there should be four tr elements to define the rows and three td elements within each of the rows, making a total of 12 td elements.
• cellpadding - determines the empty space, in pixels,the cell’s border and the table element, the default is usually about 1.

Example 5 - Image

• Note that the syntax of inserting a moving image is no different from a non-moving image.
• The img tag is used to put an image in an HTML document.
• The src attribute tells the browser where to find the image.
• The width and height attributes are necessary because if they are excluded, the browser will tend to calculate the size as the image loads, instead of when the page loads, which means that the layout of the document may jump around while the page is loading.
• The alt attribute is the alternative description. This is an accessibility consideration, providing meaningful information for users who are unable to see the image.

For more tutorials you can  click here :)
thank you..

EASIER WAY TO DO MATHEMATICS IN COMPUTER



Maple helps analyze, explore, visualize, and solve mathematical problems quickly, easily, accurately.

what is maple?

Maple is a powerful mathematical software package, also know as a Computer Algebra System (CAS), that facilitates symbolic mathematics. Maple was first developed in 1980 by the Symbolic Computation Group at the University of Waterloo in Waterloo, Ontario, Canada. The core functionality of a CAS is manipulation of mathematical expressions in symbolic form. Maple performs mathematical computations and manipulations to solve problems from various disciplines of science.

Maple is an ideal software for students enrolled in Mathematics and other Sciences (physics, chemistry, biology, engineering, business, Economics). Maple can be used to carry out both symbolic and numerical calculations of problems in arithmetic, algebra, and calculus.  Maple can also be used to solve complex math and science problems with simple point and click interfaces. Using Maple to do your calculations and solve your math homework should make your work more interesting. 

Here are a few very simple examples:

Expression	Maple  Command	Maple Output
the integral of sin(x) with respect to x	int(cos(x),x);	sin(x)
the sum of  2 to -kth power for k=0 to infinity	sum('1/(2^k)','k'=0...infinity;	2
the derivative of the log of x squared	diff(log(x^2),x);	2/x
the solution of x*x - 3x + 2 = 0	solve(x^2 - 3*x + 2 = 0);	2,1

table 1.1

example 1.1

For more information  visit : http://www.maplesoft.com

 

Thank you for visiting. Feel free to drop your comment   :)