Protein Data Bank (PDB)

What is Protein Data Bank (PDB)?

• 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.
• Structures are available for many of the proteins and nucleic acids involved in the central processes of life, so you can go to the PDB archive to find structures for ribosomes, oncogenes, drug targets, and even whole viruses.

Click on the link below to view a PDB archive:

                                   http://www.rcsb.org/pdb/home/home.do

 

Below are the examples of proteins and their descriptions :

Name of protein	Molecule	Polymer	Chains	Length
 Amylase	ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE	1	A	425
Trypsin	BETA-TRYPSIN	1	E	223
Pepsin	PEPSIN	1	A	326
HTRA	Putative serine protease	1	A	134
Carboxypeptidase	CARBOXYPEPTIDASE A	1	A, B, D, E	307

S.M.I.L.E.S. For Dummies

INTRODUCTION

SMILES stands for Simplified Molecular Input Line Entry System. It is a specification in a form of line notation which describes 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

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.


EXAMPLES

Atoms: Atoms are represented by standard abbreviation of chemical elements in square brackets, for example [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.

For an atom holding one or more electrical charges is  it can be shown  by the sign '+' for a positive charge or by '-' for a negative charge.

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).

Aromatic: C, O, S and N atoms are shown in their lower case 'c', 'o', 's' and 'n' respectively. Benzene, pyridine and furan can be represented respectively by the SMILES c1ccccc1, n1ccccc1 and o1cccc1. Bonds between aromatic atoms are, by default, aromatic although these can be specified explicitly using the ':' symbol. Aromatic atoms can be singly bonded to each other and biphenyl can be represented by c1ccccc1-c2ccccc2. Aromatic nitrogen bonded to hydrogen, as found in pyrrole must be represented as [nH] and imidazole is written in SMILES notation as n1c[nH]cc1.

 

 

Visualization of 3-cyanoanisole as COc(c1)cccc1C#N

 

 

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.

Stereochemistry: Configuration around double bonds is specified using the characters "/" and "\". For example, F/C=C/F (see depiction) is one representation of trans-difluoroethene, in which the fluorine atoms are on opposite sides of the double bond, whereas F/C=C\F (see depiction) is one possible representation of cis-difluoroethene, in which the Fs are on the same side of the double bond, as shown in the figure.
Configuration at tetrahedral carbon is specified by @ or @@. L-Alanine, the more common enantiomer of the amino acid alanine can be written as N[C@@H](C)C(=O)O (see depiction). The @@ specifier indicates that, when viewed from nitrogen along the bond to the chiral center, the sequence of substituents hydrogen (H), methyl (C) and carboxylate (C(=O)O) appear clockwise. D-Alanine can be written as N[C@H](C)C(=O)O (see depiction). The order of the substituents in the SMILES string is very important and D-alanine can also be encoded as N[C@@H](C(=O)O)C (see depiction).

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.


APPLICATION ON SOME MOLECULES

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-]
Oenanthotoxin (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
Thiamin (C12H17N4OS+) (vitamin B1)		OCCc1c(C)[n+](=cs1)Cc2cnc(C)nc(N)2
Vanillin		O=Cc1ccc(O)c(OC)c1
Melatonin (C13H16N2O2)		CC(=O)NCCC1=CNc2c1cc(OC)cc2
Nicotine (C10H14N2)		CN1CCC[C@H]1c2cccnc2

Learn XML

           About 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

 

Below is the example of XML document :

XML does not do anything. It was created to structure, store, and transport information.

The Difference between XML and HTML

XML	HTML
displaying information	carrying information

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 documents form a tree structure that starts at "the root" and branches to "the leaves".
• Below is the example of XML document and simple syntax :

XML documents use a self-describing and simple syntax:

• The first line on the above example is the  XML declaration.
• The highlighted word describes the root element of the document (like saying: "this document is a   note"), while the code in the middle describe 4 child elements of the root (to, from, heading, and body).

XML Document Form a Tree Structure

 

• XML documents must contain a root element. This element is "the parent" of all other elements.
• The elements in an XML document form a document tree. The tree starts at the root and branches to the lowest level of the tree.
• All elements can have sub elements (child elements):

This an example of tree structure :

• To view more detail about XML tree structure you can visit this web XML Tree structure .

• In HTML, some elements do not have to have a closing tag :

                 <p>This is a paragraph.

                < br>

 

• But in XML, it is illegal to omit the closing tag. All elements must have a closing tag:

 

                <p>This is a paragraph.</p>
                < br />
 

•  XML tags are case sensitive. The tag <Letter> is different from the tag <letter>.
• Opening and closing tags must be written with the same case :

 

 

 

Internet History TIMELINE

Internet History Timeline

Early research and development: 1961 (1961) – First packet-switching papers 1966 (1966) – Merit Network founded 1966 (1966) – ARPANET planning starts 1969 (1969) – ARPANET carries its first packets 1970 (1970) – Mark I network at NPL (UK) 1970 (1970) – Network Information Center (NIC) 1971 (1971) – Merit Network's packet-switched network operational 1971 (1971) – Tymnet packet-switched network 1972 (1972) – Internet Assigned Numbers Authority (IANA) established 1973 (1973) – CYCLADES network demonstrated 1974 (1974) – Telenet packet-switched network 1976 (1976) – X.25 protocol approved 1978 (1978) – Minitel introduced 1979 (1979) – Internet Activities Board (IAB) 1980 (1980) – USENET news using UUCP 1980 (1980) – Ethernet standard introduced 1981 (1981) – BITNET established

Merging the networks and creating the Internet: 1981 (1981) – Computer Science Network (CSNET) 1982 (1982) – TCP/IP protocol suite formalized 1982 (1982) – Simple Mail Transfer Protocol (SMTP) 1983 (1983) – Domain Name System (DNS) 1983 (1983) – MILNET split off from ARPANET 1985 (1985) – First .COM domain name registered 1986 (1986) – NSFNET with 56 kbit/s links 1986 (1986) – Internet Engineering Task Force (IETF) 1987 (1987) – UUNET founded 1988 (1988) – NSFNET upgraded to 1.5 Mbit/s (T1) 1988 (1988) – OSI Reference Model released 1988 (1988) – Morris worm 1989 (1989) – Border Gateway Protocol (BGP) 1989 (1989) – PSINet founded, allows commercial traffic 1989 (1989) – Federal Internet Exchanges (FIXes) 1990 (1990) – GOSIP (without TCP/IP) 1990 (1990) – ARPANET decommissioned 1990 (1990) – Advanced Network and Services (ANS) 1990 (1990) – UUNET/Alternet allows commercial traffic 1990 (1990) – Archie search engine 1991 (1991) – Wide area information server (WAIS) 1991 (1991) – Gopher 1991 (1991) – Commercial Internet eXchange (CIX) 1991 (1991) – ANS CO+RE allows commercial traffic 1991 (1991) – World Wide Web (WWW) 1992 (1992) – NSFNET upgraded to 45 Mbit/s (T3) 1992 (1992) – Internet Society (ISOC) established 1993 (1993) – Classless Inter-Domain Routing (CIDR) 1993 (1993) – InterNIC established 1993 (1993) – Mosaic web browser released 1994 (1994) – Full text web search engines 1994 (1994) – North American Network Operators' Group (NANOG) established

Commercialization, privatization, broader access leads to the modern Internet: 1995 (1995) – New Internet architecture with commercial ISPs connected at NAPs 1995 (1995) – NSFNET decommissioned 1995 (1995) – GOSIP updated to allow TCP/IP 1995 (1995) – very high-speed Backbone Network Service (vBNS) 1995 (1995) – IPv6 proposed 1998 (1998) – Internet Corporation for Assigned Names and Numbers (ICANN) 1999 (1999) – IEEE 802.11b wireless networking 1999 (1999) – Internet2/Abilene Network 1999 (1999) – vBNS+ allows broader access 2000 (2000) – Dot-com bubble bursts 2001 (2001) – New top-level domain names activated 2001 (2001) – Code Red I, Code Red II, and Nimda worms 2003 (2003) – UN World Summit on the Information Society (WSIS) phase I 2003 (2003) – National LambdaRail founded 2004 (2004) – UN Working Group on Internet Governance (WGIG) 2005 (2005) – UN WSIS phase II 2006 (2006) – First meeting of the Internet Governance Forum 2010 (2010) – First internationalized country code top-level domains registered 2012 (2012) – ICANN begins accepting applications for new generic top-level domain names

Examples of popular Internet services: 1990 (1990) – IMDb Internet movie database 1995 (1995) – Amazon.com online retailer 1995 (1995) – eBay online auction and shopping 1995 (1995) – Craigslist classified advertisements 1996 (1996) – Hotmail free web-based e-mail 1997 (1997) – Babel Fish automatic translation 1998 (1998) – Google Search 1998 (1998) – Yahoo! Clubs (now Yahoo! Groups) 1998 (1998) – PayPal Internet payment system 1999 (1999) – Napster peer-to-peer file sharing 2001 (2001) – BitTorrent peer-to-peer file sharing 2001 (2001) – Wikipedia, the free encyclopedia 2003 (2003) – LinkedIn business networking 2003 (2003) – Myspace social networking site 2003 (2003) – Skype Internet voice calls 2003 (2003) – iTunes Store 2003 (2003) – 4Chan Anonymous image-based bulletin board 2003 (2003) – The Pirate Bay, torrent file host 2004 (2004) – Facebook social networking site 2004 (2004) – Podcast media file series 2004 (2004) – Flickr image hosting 2005 (2005) – YouTube video sharing 2005 (2005) – Reddit link voting 2005 (2005) – Google Earth virtual globe 2006 (2006) – Twitter microblogging 2007 (2007) – WikiLeaks anonymous news and information leaks 2007 (2007) – Google Street View 2007 (2007) – Kindle, e-book reader and virtual bookshop 2008 (2008) – Amazon Elastic Compute Cloud (EC2) 2008 (2008) – Dropbox cloud-based file hosting 2008 (2008) – Encyclopedia of Life, a collaborative encyclopedia intended to document all living species 2008 (2008) – Spotify, a DRM-based music streaming service 2009 (2009) – Bing search engine 2009 (2009) – Google Docs, Web-based word processor, spreadsheet, presentation, form, and data storage service 2009 (2009) – Kickstarter, a threshold pledge system 2011 (2011) – Google+ social networking

TIMELINE

For more information, do visit the Internet Hall of Fame.

How HTML works . . ?

• HTML stands for Hypertext Markup Language. It is one of the many languages of the computer.

• A HTML code would basically have this layout:

Coding for list:

Replace the " text " and with your own words and 

• For a bullet listing, you may use this code:

<html>

<body>

<h4>Enter Your Title :</h4>

<ul type="disc">

 <li>text</li>

 <li>text</li>

 <li>text</li>

 <li>text</li>

</ul>

</body>

</html>

• The code will look like this :

• For a number listing, you may use this code:

<html>
<body>
<h4>Enter Your Title :</h4>
<ol type "A">
 <li>text</li>
 <li>text</li>
 <li>text</li>
 <li>text</li>
</ol>
</body>
</html>

• The code will look like this image below :

• For a nested listing, you may use this code:

<html>
<body>
<h4>Enter Your Title :</h4>
<ul>
 <li>text</li>
 <li>text  <ul>
  <li>text</li>
  <li>text</li>
  </ul>
 </li>
 <li>text</li>
</body>
</html>

This code will looks like this :

Coding for Link :

• To create a link , you can copy this image :

<html>
<body>
<p>
<a href="insert link here">insert text to display</a>
</p>
</body>
</html>

This is an example of  link.

Coding for table :

• For no cell padding, you may use this code:

<html>
<body>
<h4>Insert title for table:</h4>
<table border="1">
<tr>
 <td>First</td>
 <td>Row</td>
</tr>
<tr>
 <td>Second</td>
 <td>Row</td>
</tr>
</table>
</body>
</html>

Example table :

First	Row
Second	Row

• For cell padding, you may use this code:

<html>
<body>
<h4>Insert title for table:</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>

Example table :

First	Row
Second	Row

Coding for non-moving and moving picture :

<html>
<body>
<p>
An image :
<img src="insert URL for image" alt="insert picture name here"width="32" height="32" />
</p>
</body>
</html>

It will looks like this image below :

Example of non-moving and moving picture

To learn more about HTML coding, you can visit the w3schools  website for more information. Good luck in trying ! :)

How To Download Maple

                                                                    WHAT IS MAPLE ?

Maple, first released in 1981 by Waterloo Maple, Inc., is a system for doing mathematics on a computer. Maple combines symbolic manipulation, numerical mathematics, outstanding graphics, and a sophisticated programming language. Because of its versatility, Maple has established itself as the computer algebra system of choice for many computer users including commercial and government scientists and engineers, mathematics, science, and engineering teachers and researchers, and students enrolled in mathematics, science, and engineering courses.In maple there are two function which is text and math. Text is use to write anything in maple without been calculated. While math is use when users want to calculate something. Below is how text is used.

To calculate equation in maple, users have to know it code.Users also can use templates that is already exist in the maple. There is also maple help that can help user to use the maple. Below is the example of its interface.

 

 

 

  HOW TO DOWNLOAD MAPLE ?

 

    These are the few steps on how to download Maple :

1. Go to http://softarchive.net/blogs/leeman/maplesoft_maple.1243429.html
    
2. Then , you will see this picture

 

          click on,

Some of the Many Functions Known To Maple Include:

Function Command cos x cos(x) sin x sin(x) tan x tan(x) cot x cot(x) arccos x arccos(x) arcsin x arcsin(x) arctan x arctan(x)

Function Command arccot x arccot(x) ex exp(x) ln x log(x) cosh x cosh(x) sinh x sinh(x) tanh x tanh(x) arcsinh x arcsinh(x)

 

 

In order to help user to understand better the usage of maple, there has been published book about maple. This book can really help students to understand better the usage of maple.

 

 

 

 Thanks for reading. Good luck in trying ! :)