Wednesday, 11 December 2013



Protein Data Bank


The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecules, such as proteins 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 overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
The PDB is a key resource in areas of structural biology, such as structural genomics. Most major scientific journals, and some funding agencies, such as the NIH in the USA, now require scientists to submit their structure data to the PDB. If the contents of the PDB are thought of as primary data, then there are hundreds of derived (i.e., secondary) databases that categorize the data differently. For example, both SCOP and CATH categorize structures according to type of structure and assumed evolutionary relations; GO categorize structures based on genes.

These are the link  for some Protein Data Bank website

How do data information is stored in form of data query?


Search Field
Example
PDB ID
4HHB, 2MHR
Deposition/Release Date
September 1 1996
Contain Chain Type
Protein: Ignore, Enzyme: Yes, DNA
Citation Author
S.S. Taylor

Here are some examples of the protein:

 HtrA

Molecule:Putative serine protease
Polymer:1Type:protein

Chains:A
Fragment:PDZ domain, UNP residues 266-390
OrganismStreptococcus pneumoniae
Gene NameSP_2239

 Aminopeptidase

Molecule:METHIONINE AMINOPEPTIDASE
Polymer:1Type:protein

Chains:A
EC#:3.4.11.18   
Details:COMPLEX WITH T-BUTANOL AND COBALT
OrganismHomo sapiens
Gene NamesMETAP2 MNPEP P67EIF2


 Carboxypeptidase

Molecule:CARBOXYPEPTIDASE A
Polymer:1Type:protein

Chains:A
EC#:3.4.17.1   
OrganismBos taurus
Gene NamesCPA1 CPA


 Collagenase

Molecule:COLLAGENASE
Polymer:1Type:protein

Chains:A
EC#:3.4.24.3   
Fragment:RESIDUES 119-880
OrganismClostridium histolyticum
Gene NamecolG


Subsitilin

Molecule:Tk-subtilisin
Polymer:1Type:protein

Chains:A
Mutation:S324A, D372A
OrganismThermococcus kodakarensis KOD1
Gene NameTK1675





Enjoy Learning The Protein

















Tuesday, 10 December 2013


The Simplified Molecular-Input Line-Entry System or SMILES is a specification in form of a line notation for describing the structure of chemical molecules using short ASCII strings ASCII. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules.

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.


The term Canonical 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 while The term Isomeric SMILES refers to the version of the SMILES specification that includes extensions to support the specification of isotopes,  chirality, and configuration about double bonds.


Graph-based Definition
In terms of a graph-based computational procedure, SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. The chemical graph is first trimmed to remove hydrogen atoms and cycles are broken to turn it into a spanning tree. Where cycles have been broken, numeric suffix labels are included to indicate the connected nodes. Parentheses are used to indicate points of branching on the tree.

There are some examples of SMILES bonds that can be use:

SMILES BONDS
SYMBOL
SINGLE
-
DOUBLE
=
TRIPLE
#


There are also some example of SMILES and their names:

SMILES
NAME
CC
Ethane
O=C=O
Carbon dioxide
C#N
Hydrogen cyanide
CCN(CC)CC
Triethylamine

Here are some links for tutorial on how to use SMILES:

Here are the examples of SMILES notation using Chemsketch:



Example of complex SMILES using Chemsketch:



HAVE FUN LEARNING SMILES :)


Wednesday, 27 November 2013

ChemSketch






ACD/ChemSketch Freeware is a drawing package that allows users to draw chemical structures including organics, organometallics, polymers, and Markush structures. It also includes features such as calculation of molecular properties (e.g., molecular weight, density, molar refractivity etc.), 2D and 3D structure cleaning and viewing, functionality for naming structures (fewer than 50 atoms and 3 rings), and prediction of logPIt also act as an additional toolsACD/Labs software aids in teaching key chemistry concepts to high school, undergraduate, and graduate chemistry students. In addition, students benefit from exposure in the learning environment to the same tools they will encounter in the workforce.


ACD/ChemBasic is a simple, convenient, and functionally rich programming language for the presentation and manipulation of molecular structure and related objects through ACD/Labs' software. ACD/ChemBasic allows you to customize ACD/Labs software for your own purposes, to automate routine tasks, or to interface your own programs with ACD/Labs software.
You can use ACD/Chem Basic to:
  1. Write simple macros that automate routine operations within ACD/Labs software
  2. Extend the functionality of ACD/Labs software to suit your particular needs such as integrating with an external program
Because ACD/ChemBasic is a superset of Basic, it is easy to learn and easy to use; consisting of common statements and functions for dealing with numbers or texts, built-in molecular objects and functions to manipulate them, and the objects and functionality of ACD/Labs programs.

The latest version of ACD Chemsketch is version 14.0:

Publisher Advanced Chemistry Development
Publisher web site http://www.acdlabs.com/
Release date November 07, 2013
Operating systems Windows 7, Windows 8, Windows XP
Category Educational Software



There are several links to download this ACD Chemsketch



Here are some links for the tutorial on how to use ChemSketch:
It also can be used to draw complex organic molecule:


Wednesday, 20 November 2013


INTRODUCTION


What is XML?

       XML stands for Extensible Markup Language and it is a markup language like HTML. Although it similar to HTML it was designed to carry data, not to display data. XML tags are not predefined as it required an individual to define their own tags. XML is designed to be self-descriptive and W3C recommendation on February 10, 1998 and it is defined in the XML 1.0 specification. 
 
       The design goals of XML emphasize simplicity, generality, and usability over the Internet. It is a textual data format with strong support via Unicode for the languages of the world. Although the design of XML focuses on documents, it is widely used for the representation of arbitrary data structures, for example in web services.
       Many application programming interfaces (APIs) have been developed to aid software developers with processing XML data, and several schema systems exist to aid in the definition of XML-based languages.
As of 2009, hundreds of document formats using XML syntax have been developed, including RSS, Atom, SOAP, and XHTML. XML-based formats have become the default for many office-productivity tools, including Microsoft Office (Office Open XML), OpenOffice.org and LibreOffice (OpenDocument), and Apple's iWork. XML has also been employed as the base language for communication protocols, such as XMPP.


The Difference Between XML and HTML

XML is not a replacement for HTML.
XML and HTML were designed with different goals:

  • XML was designed to transport and store data, with focus on what data is
  • HTML was designed to display data, with focus on how data looks

 

XML Does Not DO Anything

XML does not DO anything. It 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.

The tags in the example above (like <to> and <from>) are not defined in any XML standard. These tags are "invented" by the author of the XML document.
That is because the XML language has no predefined tags.
The tags used in HTML are predefined. HTML documents can only use tags defined in the HTML standard (like <p>, <h1>, etc.).
XML allows the author to define his/her own tags and his/her own document structure.


There are tutorial link on how to use XML



There are some example of XML


 Figure 1






 Figure 2






 These XML also can be converted into table


 <bookstore>
<book category="COOKING">
<title lang="en">Everyday Italian</title>

<author>Giada De Laurentiis</author>
<year>2005</year>
<price>RM 30.00</price>
</book><book category="CHILDREN">
<title lang="en">Harry Potter</title>
<author>J K. Rowling</author>
<year>2005</year>
<price>RM 29.99</price>
</book>



Bookcategory Title Author Year Price
Cooking Everyday Italian Giada De Laurentis 2005 RM 30.00
Children Harry Potter K. Rowling 2005 RM 29.99

So, enjoy your day in learning XML

INTERNET HISTORY AND GROWTH


INTRODUCTION:
Internet is a network of networks, joining many government, university and private computers together and providing an infrastructure for the use of E-mail, bulletin boards, file archives, hypertext documents, databases and other computational resources.

Internet Timeline:
1969
ARPA (Advanced Research Projects Agency) goes online in December, connecting four major U.S. universities. Designed for research, education, and government organizations, it provides a communications network linking the country in the event that a military attack destroys conventional communications systems.
1972
Electronic mail is introduced by Ray Tomlinson, a Cambridge, Mass., computer scientist. He uses the @ to distinguish between the sender's name and network name in the email address.
1973
Transmission Control Protocol/Internet Protocol (TCP/IP) is designed and in 1983 it becomes the standard for communicating between computers over the Internet. One of these protocols, FTP (File Transfer Protocol), allows users to log onto a remote computer, list the files on that computer, and download files from that computer.
1976
Presidential candidate Jimmy Carter and running mate Walter Mondale use email to plan campaign events.
Queen Elizabeth sends her first email. She's the first state leader to do so.
1982
The word “Internet” is used for the first time.
1984
Domain Name System (DNS) is established, with network addresses identified by extensions such as .com, .org, and .edu.
Writer William Gibson coins the term “cyberspace.”
1985
Quantum Computer Services, which later changes its name to America Online, debuts. It offers email, electronic bulletin boards, news, and other information.
1988
A virus called the Internet Worm temporarily shuts down about 10% of the world's Internet servers.
1989
The World (world.std.com) debuts as the first provider of dial-up Internet access for consumers.
Tim Berners-Lee of CERN (European Laboratory for Particle Physics) develops a new technique for distributing information on the Internet. He calls it the World Wide Web. The Web is based on hypertext, which permits the user to connect from one document to another at different sites on the Internet via hyperlinks (specially programmed words, phrases, buttons, or graphics). Unlike other Internet protocols, such as FTP and email, the Web is accessible through a graphical user interface.
1990
The first effort to index the Internet is created by Peter Deutsch at McGill University in Montreal, who devises Archie, an archive of FTP sites.
1991
Gopher, which provides point-and-click navigation, is created at the University of Minnesota and named after the school mascot. Gopher becomes the most popular interface for several years.
Another indexing system, WAIS (Wide Area Information Server), is developed by Brewster Kahle of Thinking Machines Corp.
1993
Mosaic is developed by Marc Andreeson at the National Center for Supercomputing Applications (NCSA). It becomes the dominant navigating system for the World Wide Web, which at this time accounts for merely 1% of all Internet traffic.
1994
The White House launches its website, www.whitehouse.gov.
Initial commerce sites are established and mass marketing campaigns are launched via email, introducing the term “spamming” to the Internet vocabulary.
Marc Andreessen and Jim Clark start Netscape Communications. They introduce the Navigator browser.
1995
CompuServe, America Online, and Prodigy start providing dial-up Internet access.
Sun Microsystems releases the Internet programming language called Java.
The Vatican launches its own website, www.vatican.va.
1996
Approximately 45 million people are using the Internet, with roughly 30 million of those in North America (United States and Canada), 9 million in Europe, and 6 million in Asia/Pacific (Australia, Japan, etc.). 43.2 million (44%) U.S. households own a personal computer, and 14 million of them are online.
1997
On July 8, 1997, Internet traffic records are broken as the NASA website broadcasts images taken by Pathfinder on Mars. The broadcast generates 46 million hits in one day.
The term “weblog” is coined. It’s later shortened to “blog.”
1998
Google opens its first office, in California.
1999
College student Shawn Fanning invents Napster, a computer application that allows users to swap music over the Internet.
The number of Internet users worldwide reaches 150 million by the beginning of 1999. More than 50% are from the United States.
“E-commerce” becomes the new buzzword as Internet shopping rapidly spreads.
MySpace.com is launched.
2000
To the chagrin of the Internet population, deviant computer programmers begin designing and circulating viruses with greater frequency. “Love Bug” and “Stages” are two examples of self-replicating viruses that send themselves to people listed in a computer user's email address book. The heavy volume of email messages being sent and received forces many infected companies to temporarily shut down their clogged networks.
The Internet bubble bursts, as the fountain of investment capital dries up and the Nasdaq stock index plunges, causing the initial public offering (IPO) window to slam shut and many dotcoms to close their doors.
America Online buys Time Warner for $16 billion. It’s the biggest merger of all time.
2001
Napster is dealt a potentially fatal blow when the 9th U.S. Circuit Court of Appeals in San Francisco rules that the company is violating copyright laws and orders it to stop distributing copyrighted music. The file-swapping company says it is developing a subscription-based service.
About 9.8 billion electronic messages are sent daily.
Wikipedia is created.
2002
As of January, 58.5% of the U.S. population (164.14 million people) uses the Internet. Worldwide there are 544.2 million users.
The death knell tolls for Napster after a bankruptcy judge ruled in September that German media giant Bertelsmann cannot buy the assets of troubled Napster Inc. The ruling prompts Konrad Hilbers, Napster CEO, to resign and lay off his staff.
2003
It's estimated that Internet users illegally download about 2.6 billion music files each month.
Spam, unsolicited email, becomes a server-clogging menace. It accounts for about half of all emails. In December, President Bush signs the Controlling the Assault of Non-Solicited Pornography and Marketing Act of 2003 (CAN-SPAM Act), which is intended to help individuals and businesses control the amount of unsolicited email they receive.
Apple Computer introduces Apple iTunes Music Store, which allows people to download songs for 99 cents each.
Spam, unsolicited email, becomes a server-clogging menace. It accounts for about half of all emails.
Apple Computer introduces Apple iTunes Music Store, which allows people to download songs for 99 cents each.
2004
Internet Worm, called MyDoom or Novarg, spreads through Internet servers. About 1 in 12 email messages are infected.
Online spending reaches a record high—$117 billion in 2004, a 26% increase over 2003.
2005
YouTube.com is launched.
2006
There are more than 92 million websites online.
2007
Legal online music downloads triple to 6.7 million downloads per week.
Colorado Rockies' computer system crashes when it receives 8.5 million hits within the first 90 minutes of World Series ticket sales.
The online game, World of Warcraft, hits a milestone when it surpasses 9 million subscribers worldwide in July.
2008
In a move to challenge Google's dominance of search and advertising on the Internet, software giant Microsoft offers to buy Yahoo for $44.6 billion.
In a San Fransisco federal district court, Judge Jeffrey S. White orders the disabling of Wikileaks.org, a Web site that discloses confidential information. The case was brought by Julius Baer Bank and Trust, located in the Cayman Islands, after a disgruntled ex-employee allegedly provided Wikileaks with stolen documents that implicate the bank in asset hiding, money laundering, and tax evasion. Many web communities, who see the ruling as unconstitutional, publicized alternate addresses for the site and distributed bank documents through their own networks. In response, Judge White issues another order to stop the distribution of bank documents.
Microsoft is fined $1.3 billion by the European Commission for further abusing its dominant market position, and failing to comply to their 2004 judgment, which ordered Microsoft to give competitors information necessary to operate with Windows. Since 2004, Microsoft has been fined a total of $2.5 billion by the Commission for not adhering to their ruling.
2012
A major protest online in January shakes up Congressional support for anti-Web piracy measures. The protest, including a 24-hour shutdown of the English-language Wikipedia site, is over two bills, the Stop Online Piracy Act in the House and the Protect IP Act in the Senate. The main goal of both bills is to stop illegal downloading and streaming of TV shows and movies online. The tech industry is concerned that the bills will give media companies too much power to shut down website.
 
Can read more at this site:
click here 

The Universal Resource Locator (URL)
A uniform resource locator, abbreviated URL, also known as web address, is a specific character string that constitutes a reference to a resource. In most web browsers, the URL of a web page is displayed on top inside an address bar. An example of a typical URL would be "http://en.example.org/wiki/Main_Page".

Protocols:
Some protocols that may appear in url are:
Protocol Names Use
ftp:// File transfer
http:// Hypertext
https:// Hypertext secure
telnet:// Remote login

Domain names:
A domain name is an identification string that defines a realm of administrative autonomy, authority, or control on the Internet. Domain names are formed by the rules and procedures of the Domain Name System (DNS). Any name registered in the DNS is a domain name.
The top-level domains (TLDs) are the highest level of domain names of the Internet. Top-level domains form the DNS root zone of the hierarchical Domain Name System. Every domain name ends with a top-level domain label.
Example of top-level domain:

Top-level domain Stands for
.com company
.edu education
.info information

Domain Name System(DNS):
The Domain Name System (DNS) is a hierarchical distributed naming system for computers, services, or any resource connected to the Internet or a private network. It associates various information with domain names assigned to each of the participating entities. Most prominently, it translates easily memorized domain names to the numerical IP addresses needed for the purpose of locating computer services and devices worldwide. By providing a worldwide, distributed keyword-based redirection service, the Domain Name System is an essential component of the functionality of the Internet.

Internet Address(IP):

An Internet address, known as an IP address for “Internet Protocol” is comprised of four binary octets, making it a 32-bit address. IP addresses, difficult for humans to read in binary format, are often converted to “dotted decimal format” To convert the 32-bit binary address to dotted decimal format, divide the address into four 8-bit octets and then convert each octet to a decimal number. Each octet will have one of 256 values (0 through 255)

192.48.29.253
 (Example of an IP address in dotted decimal form)
 
IP address conversion:
1) Divide the IP address into four octets
 01011110 00010100 11000011 11011100 
2) Convert each binary octet into a decimal number
01011110 = 64+16+8+4+2 = 94 
00010100 = 16+4 = 20
11000011 = 128+64+2+1 = 195 
11011100 = 128+64+16+8+4 = 220
 3) Write out the decimal values separated by periods 
94.20.195.220
 
To learn more about IP you can click here.
 
HAVE FUN LEARNING AND USE THE INTERNET!!!!  
 

Wednesday, 13 November 2013

HTML


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 presentational HTML.
There are some web that provide tutorial for using HTML.
This is an example how to write in HTML language.

How to make a table using HTML:

The result will be like this:

Without cellpadding:

First Row
Second Row

With cellpadding:

First Row
Second Row

Enjoy doing HTML