Simplified molecular-input line-entry system(SMILES)

 

 

For further inquiry..

http://www.daylight.com/meetings/summerschool98/course/dave/smiles-intro.html

http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

http://chemical-quantum-images.blogspot.com/2008/03/simplified-molecular-input-line-entry.html

•  is a specification in form of a line notation for 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
• 

 

 

 

Graph-based definition

 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

 

 

Atoms

 

 

 

Atoms are represented by the standard abbreviation of the chemical elements, in square brackets, such as [Au] for gold. Brackets can be omitted for the "organic subset" of B, C, N, O, P, S, F, Cl, Br, and I. All other elements must be enclosed in brackets. If the brackets are omitted, the proper number of implicit hydrogen atoms is assumed; for instance the SMILES for water is simply O.
An atom holding one or more electrical charges is enclosed in brackets, followed by the symbol H if it is bonded to one or more atoms of hydrogen, followed by the number of hydrogen atoms (as usual one is omitted example: NH4 for ammonium), then by the sign '+' for a positive charge or by '-' for a negative charge. The number of charges is specified after the sign (except if there is one only); however, it is also possible write the sign as many times as the ion has charges: instead of "Ti+4", one can also write "Ti++++" (Titanium IV, Ti⁴⁺). Thus, the hydroxide anion is represented by [OH-], the oxonium cation is [OH3+] and the cobalt III cation (Co³⁺) is either [Co+3] or [Co+++].

 

 

 Bonds

 

 Bonds between aliphatic atoms are assumed to be single unless specified otherwise and are implied by adjacency in the SMILES string. For example the SMILES for ethanol can be written as CCO. Ring closure labels are used to indicate connectivity between non-adjacent atoms in the SMILES string, which for cyclohexane and dioxane can be written as C1CCCCC1 and O1CCOCC1 respectively. For a second ring, the label will be 2 (naphthalene: c1cccc2c1cccc2 (note the lower case for aromatic compounds)), and so on. After reaching 9, the label must be preceded by a '%', in order to differentiate it from two different labels bonded to the same atom (~C12~ will mean the atom of carbon holds the ring closure labels 1 and 2, whereas ~C%12~ will indicate one label only, 12). Double, triple, and quadruple bonds are represented by the symbols '=', '#', and '$' respectively as illustrated by the SMILES O=C=O (carbon dioxide), C#N (hydrogen cyanide) and [Ga-]$[As+] (gallium arsenide).

 

 

 

 Branching

 

Branches are described with parentheses, as in CCC(=O)O for propionic acid and C(F)(F)F for fluoroform. Substituted rings can be written with the branching point in the ring as illustrated by the SMILES COc(c1)cccc1C#N (see depiction) and COc(cc1)ccc1C#N (see depiction) which encode the 3 and 4-cyanoanisole isomers. Writing SMILES for substituted rings in this way can make them more human-readable.

 

 

 Isotopes

 

 Isotopes are specified with a number equal to the integer isotopic mass preceding the atomic symbol. Benzene in which one atom is carbon-14 is written as [14c]1ccccc1 and deuterochloroform is [2H]C(Cl)(Cl)Cl.

 

 

 

 

 

 

Molecule	Structure	SMILES Formula
Dinitrogen	N≡N	N#N
Methyl isocyanate (MIC)	CH3–N=C=O	CN=C=O
Copper(II) sulfate	Cu2+ SO42-	[Cu+2].[O-]S(=O)(=O)[O-]
Œnanthotoxin (C17H22O2)		CCC[C@@H](O)CC\C=C\C=C\C#CC#C\C=C\CO
Pyrethrin II (C22H28O5)		COC(=O)C(\C)=C\C1C(C)(C)[C@H]1C(=O)O[C@@H]2C(C)=C(C(=O)C2)CC=CC=C
Aflatoxin B1 (C17H12O6)		O1C=C[C@H]([C@H]1O2)c3c2cc(OC)c4c3OC(=O)C5=C4CCC(=O)5
Glucose (glucopyranose) (C6H12O6)		OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)1
Bergenin (cuscutin) (a resin) (C14H16O9)		OC[C@@H](O1)[C@@H](O)[C@H](O)[C@@H]2[C@@H]1c3c(O)c(OC)c(O)cc3C(=O)O2
A pheromone of the Californian scale insect		CC(=O)OCCC(/C)=C\C[C@H](C(C)=C)CCC=C

 

 

 

 

 

 

About the PDB Archive and the RCSB PDB

The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.

The PDB archive is available at no cost to users. The PDB archive is updated each week at the target time of Wednesday 00:00 UTC (Coordinated Universal Time). The most recent release is timestamped and linked on every page in the top right header.

The PDB was established in 1971 at Brookhaven National Laboratory and originally contained 7 structures. In 1998, the Research Collaboratory for Structural Bioinformatics (RCSB) became responsible for the management of the PDB. In 2003, the wwPDB was formed to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community. It consists of organizations that act as deposition, data processing and distribution centers for PDB data.

In addition, the RCSB PDB supports a website where visitors can perform simple and complex queries on the data, analyze, and visualize the results. Details about the history, function, progress, and future goals of the RCSB PDB can be found in our Annual Reports and Newsletters.

The PDB Advisory Notice defines the conditions for using data from the PDB archive.

RCSB PDB staff are located at Rutgers, The State University of New Jersey and the University of California, San Diego. Watch this video for a tour of the Rutgers site;

• http://www.youtube.com/watch?v=akmXIy7XQwA

Some of the protein from the RCSB Protein Data Bank (PDB)

• Amylase

Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.

• Trysin

The Geometry of the Reactive Site and of the Peptide Groups in Trypsin, Trypsinogen and its Complexes with Inhibitors.

• Pepsin

X-ray analyses of aspartic proteinases. II. Three-dimensional structure of the hexagonal crystal form of porcine pepsin at 2.3 A resolution.

• HtrA

Solution structure of HtrA PDZ domain from Streptococcus pneumoniae and its interaction with YYF-COOH containing peptides.

• Carboxypeptidase

Insight into the stereochemistry in the inhibition of carboxypeptidase A with N-(hydroxyaminocarbonyl)phenylalanine: binding modes of an enantiomeric pair of the inhibitor to carboxypeptidase A.

The RCSB Protein Data Bank: site functionality and bioinformatics use cases

Annotation	Ontology/Database	Description
Biological process	GO Consortium	Controlled vocabulary that describes biological processes
Cellular component	GO Consortium	Controlled vocabulary that describes the cellular location
Molecular function	GO Consortium	Controlled vocabulary that describes the molecular function
Enzyme classification	Enzyme Commission (EC) system recommended by the IUBMB	Classification system for the reactions catalyzed by enzymes
Transporter classification	Transporter Classification (TC) system recommended by the IUBMB	Classification system for membrane transport proteins that  incorporates both  functional and phylogenetic information
Medical subject terms	MeSH terms developed by the National Library of Medicine	Controlled vocabulary to describe medical terms;  used for indexing of PubMed abstracts
Source organism	NCBI taxonomy	A curated set of names and classifications of  organisms from superkingdoms to subspecies
Genome location	Entrez Gene	Location of genes in the genomes of various organisms for  proteins in the PDB.  The top level in the hierarchy is the organism's genome.  Each genome expands into chromosomes,  which in turn expand into a list of loci on  the chromosomes.
Fold/domain classification	SCOP	Hierarchical structural classification of proteins that  provides a  description of structural and evolutionary relationships  of proteins of known structure
Fold/domain classification	CATH	Hierarchical structural classification of protein domains.  Each protein has  been divided into structural domains and assigned  into homologous superfamilies.

Internet History

Welcome to the Internet Hall of Fame's Living History Timeline      

The Internet Hall of Fame's Living History Timeline explores the history of the Internet and highlights the inductees who have pioneered Internet technology, contributed to ongoing development and innovation and helped expand the Internet's reach across the globe

1957

 USSR Launches Sputnik USSR Launches Sputnik into space and, with it, global communications.

 

1958

Bell Labs Invents Modem Bell Labs researchers invent the modem (modulator - demodulator), which converts digital signals to electrical (analog) signals and back, enabling communication between computers.

1958

U.S. Government Creates ARPA The United States government creates the Advanced Research Projects Agency (ARPA) in response to Sputnik launch.

1961

 Leonard Kleinrock Pioneers Packet-Switching Leonard Kleinrock pioneers the packet-switching concept in his Massachusetts Institute of Technology (MIT) doctoral thesis about queueing theory: Information Flow in Large Communication Nets.



ASCII ALPHABETS

A	1000001	N	1001110
B	1000010	O	1001111
C	1000011	P	1010000
D	1000100	Q	1010001
E	1000101	R	1010010
F	1000110	S	1010011
G	1000111	T	1010100
H	1001000	U	1010101
I	1001001	V	1010110
J	1001010	W	1010111
K	1001011	X	1011000
L	1001100	Y	1011001
M	1001101	Z	1011000

 

1963

 ASCII Is Developed The first universal standard for computers, ASCII (American Standard Code for Information Exchange) is developed by a joint industry-government committee. ASCII permits machines from different manufacturers to exchange data.

1964 — 1967

Paul Baran, Donald Davies Develop Message Blocks/Packet-switching The Rand Corporation's Paul Baran develops message blocks in the U.S., while Donald Watts Davies, at the National Physical Laboratory in Britain, simultaneously creates a similar technology called packet-switching. The technology revolutionizes data communications

1965

Lawrence Roberts & Thomas Marill Create First Wide-area Network

Lawrence Roberts (MIT) and Thomas Marill get an ARPA contract to create the first wide-area network (WAN) connection via long distant dial-up between a TX-2 computer in Massachusetts and a Q-32 computer in California. The system confirms that packet switching offers the most promising model for communication between computers.

1967

ARPAnet Design Begins

Lawrence Roberts leads ARPAnet design discussions and publishes first ARPAnet design paper: "Multiple Computer Networks and Intercomputer Communication."  Wesley Clark suggests the network is managed by interconnected ‘Interface Message Processors’ in front of the major computers. Called IMPs, they evolve into today’s routers.

1968
Bolt Beranek and Newman Wins IMP Development Contract Bolt Beranek and Newman, Inc. (BBN) is awarded the ARPA contract to build the Interface Message Processors

1968

UCLA Develops ARPAnet Host Level Protocols

Steve Crocker heads UCLA Network Working Group under Professor Leonard Kleinrock to develop host level protocols for ARPAnet communication in preparation for becoming the first node.  The group, which includes Vint Cerf and Jon Postel, lays the foundation for protocols of the modern Internet.

1969
IMP Network Links First Four Nodes The physical Interface Message Processor (IMP) network is constructed, linking four nodes: University of California at Los Angeles, SRI (in Stanford), University of California at Santa Barbara, and University of Utah.

1973

            TCP/IP Protocol Development Begins Development begins on what will eventually be called TCP/IP protocol by a group headed by Vint Cerf (Stanford) and Robert Kahn (DARPA). The new protocol will allow diverse computer networks to interconnect and communicate with each other.

 1974
            Bolt Beranek and Newman Founds Telenet Lawrence Roberts helps Bolt Beranek and Newman (BBN) found Telenet, the first public packet data service, a commercial version of ARPAnet.

 

1989

Tim Berners-Lee Creates WWW

At CERN, the European Physical Laboratory, Tim Berners-Lee creates the World Wide Web. Robert Cailliau is a key proponent of the project, and helps Berners-Lee author a proposal for funding.  Later, Cailliau develops, along with Nicola Pellow, the first web browser for the Mac OS operating system.

 1990
            Linus Torvalds Creates Linux Linus Torvalds creates Linux and becomes a leading supporter of Open Source software.

1991

World Wide Web Opens to Public

The World Wide Web is made available to the public for the first time on the Internet. 

1993

NCSA Releases Mosaic Browser

The National Center for Supercomputing Applications (NCSA) releases the Mosaic browser, which helps popularize the World Wide Web among the general public.

2012
            Internet Society Founds Internet Hall of Fame The Internet Society founds the Internet Hall of Fame and the first 33 members are inducted in a ceremony in Geneva, Switzerland.



For detail information,please surf on
http://www.historyofthings.com/history-of-the-internet
http://www.internetsociety.org/internet/what-internet/history-internet/brief-history-internet
http://www.internethalloffame.org/internet-history/timeline

XML

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

Learn XML Tutorial 

PART 1
http://www.youtube.com/watch?v=qgZVAznwX38

PART 2
http://www.youtube.com/watch?v=_44DPLiCFa0

PART 3
http://www.youtube.com/watch?v=TZNwte5MZaY

PART 4
http://www.youtube.com/watch?v=PYHMqvARNkA

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

HTML is about displaying information, while XML is about carrying information.

HTML	XML
For display	for data stucture
no knowledge of data	presentatation independent
standard	open language
case sensitive	case sensitive

 

With XML You Invent Your Own Tags

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.

(Unicode) character

By definition, an XML document is a string of characters. Almost every legal Unicode character may appear in an XML document.

Processor and application

The processor analyzes the markup and passes structured information to an application. The specification places requirements on what an XML processor must do and not do, but the application is outside its scope. The processor (as the specification calls it) is often referred to colloquially as an XML parser.

Markup and content

The characters making up an XML document are divided into markup and content, which may be distinguished by the application of simple syntactic rules. Generally, strings that constitute markup either begin with the character < and end with a >, or they begin with the character & and end with a ;. Strings of characters that are not markup are content. However, in a CDATA section, the delimiters <![CDATA[ and ]]> are classified as markup, while the text between them is classified as content. In addition, whitespace before and after the outermost element is classified as markup.

Tag

A markup construct that begins with < and ends with >. Tags come in three flavors:

• start-tags; for example: <section>
• end-tags; for example: </section>
• empty-element tags; for example: <line-break />

Element

A logical document component which either begins with a start-tag and ends with a matching end-tag or consists only of an empty-element tag. The characters between the start- and end-tags, if any, are the element's content, and may contain markup, including other elements, which are called child elements. An example of an element is<Greeting>Hello, world.</Greeting> (see hello world). Another is <line-break />.

What is an XML Element?

An XML element is everything from (including) the element's start tag to (including) the element's end tag.

An element can contain:

• other elements
• text
• attributes
• or a mix of all of the above...

<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>

In the example above, <bookstore> and <book> have element contents, because they contain other elements. <book> also has an attribute (category="CHILDREN"). <title>, <author>, <year>, and <price> have text content because they contain text.

Attribute

A markup construct consisting of a name/value pair that exists within a start-tag or empty-element tag. In the example (below) the element img has two attributes, src and alt:

<img src="madonna.jpg" alt='Foligno Madonna, by Raphael'/>

Another example would be

<step number="3">Connect A to B.</step>

where the name of the attribute is "number" and the value is "3".

An XML attribute can only have a single value and each attribute can appear at most once on each element. In the common situation where a list of multiple values is desired, this must be done by encoding the list into a well-formed XML attribute with some format beyond what XML defines itself. Usually this is either a comma or semi-colon delimited list or, if the individual values are known not to contain spaces,a space-delimited list can be used.

<div class="inner greeting-box" >Hello!</div>

where the attribute "class" has both the value "inner greeting-box", indicating the CSS class names "inner" and "greeting-box".

XML declaration

XML documents may begin by declaring some information about themselves, as in the following example:

<?xml version="1.0" encoding="UTF-8"?>

What is XML Used For?

XML is one of the most widely-used formats for sharing structured information today: between programs, between people, between computers and people, both locally and across networks.

A short example:

<part number="1976">
  <name>Windscreen Wiper</name>
  <description>The Windscreen wiper
    automatically removes rain
    from your windscreen, if it
    should happen to splash there.
    It has a rubber <ref part="1977">blade</ref>
    which can be ordered separately
    if you need to replace it.
  </description>
</part>

XML Does Not DO Anything

Maybe it is a little hard to understand, but 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:

XML Document Example

<?xml version="1.0"?>

<note>

    <to>Tove</to>

    <from>Jani</from>

    <heading>Reminder</heading>

    <body>Don't forget me this weekend!</body>

</note>

Webpages are written in HTML - a simple scripting language.

HTML is short for HyperText Markup Language.

• Hypertext is simply a piece of text that works as a link.



• Markup Language is a way of writing layout information within documents.

Basically an HTML document is a plain text file that contains text and nothing else. When a browser opens an HTML file, the browser will look for HTML codes in the text and use them to change the 

• layout, 
• insert images
• create links to other pages and you can make your own Website.

Since HTML documents are just text files they can be written in even the simplest text editor.

A more popular choice is to use a special HTML editor - maybe even one that puts focus on the visual result rather than the codes - a so-called WYSIWYG editor ("What You See Is What You Get").

Some of the most popular HTML editors, such as FrontPage or Dreamweaver will let you create pages more or less as you write documents in Word or whatever text editor you're using.

http://www.echoecho.com/htmlbasics.htm
http://www.w3schools.com/html/html_basic.asp

#TUTORIAL 1#

~Basically HTML webpage have  page stucture 

~PAGE STRUCTURE HTML consist of

1. Head-do not show directly on the page
2. Body -are shown directly on the page

Finally, all webpages have an <html> tag at the beginning and </html> the end, telling the browser where the document starts and where it stops.

For example..the basic coding ,

<html>
<body>

<h1>My First Heading<?h1>
<p>My First paragraph.<p/>

</body>

</html>

the result show like this->

My First Heading

 My First paragraph.

#TUTORIAL2 #

how to make different kinds of bulleted lists. You have the following bullet options: disc circle square

#TUTORIAL3 #

 how to make different kinds of numbered lists.

You have the following number options:

• Plain numbers


• Capital Letters


• Small Letters


• Capital Roman Numbers


• Small Roman Numbers

#TUTORIAL4 #

how to make a link.

The tags used to produce links are the <a> and </a>. 

The <a> tells where the link should start and the </a> indicates where the link ends.

Everything between these two will work as a link.

The target of the link is added to the <a> tag using 
the href="http://www.whateverpage.com" setting.

For example..the coding ,

<html>
<body>
<p>
<a href="#C4">See also Chapter 4.</a>
</p>

<h2>Chapter 1</h2>
</body>
</html>

the result show like this->

See also Chapter 4.

Chapter 1

This explains .......

#TUTORIAL5#

how to put an image.

For example..the coding ,

<html>

<body>

<p>

An image:

<img src="http://www.kelownarealestate.com/Docs/COL504Docs/Submit/House_Moving.jpg" alt="Smiley face" width="32"

height="32" />

</p>

<p>

A moving image:

<img src="http://www.netanimations.net/Moving-picture-green-skeleton-animated-gif.gif"alt="Computer man"

width="48" height="48"/>

</p>

<p>

Note that the syntax of inserting a moving image

is no different from a non-moving image

</p>

</body>

</html>

the result show like this->

 An image:
A moving image:
Note that the syntax of inserting a moving image is no different from a non-moving image 

#TUTORIAL6 #

how to make a table

Tables are defined with the <table> tag

For example..the coding ,


<html>
<body>

<h4>Without cellpadding:</h4>
<table border="1">
<tr>
  <td>First</td>
  <td>Row</td>
</tr>
<tr>
  <td>Second</td>
  <td>Row</td>
</tr>
</table>

<h4>With cellpadding:</h4>
<Table border="1"
cellpadding="10">
<tr>
 <td>First</td>
 <td>Row</td>
</tr>
<tr>
 <td>Second</td>
 <td>Row</td>
</tr>
</table>

</body>

</html>

the result show like this->

Without cellpadding:

First	Row
Second	Row

With cellpadding:

First	Row
Second	Row

Row _ _ _ and Column -

                                                  -

                                                  -

You can divide rows into columns with <td> and </td> tags

<h4>Without cellpadding:</h4>
<table border="1">

<tr>
  <td>First</td>
  <td>Row</td>
</tr>
<tr>
  <td>Second</td>
  <td>Row</td>
</tr>

To add rows to your table use the <tr> and </tr> tags.

<h4>Without cellpadding:</h4>
<table border="1">

<tr>
  <td>First</td>
  <td>Row</td>
</tr>
<tr>
  <td>Second</td>
  <td>Row</td>
</tr>

Without cellpadding:

First	Row
Second	Row