December 2012 | DYNAMIC DUO KOS1110

Sunday 23 December 2012

Protein Data Bank

What is Protein Data Bank?

A repository for 3-D biological macromolecular structure.
It is obtained by using crystallography or NMR spectroscopy.
Founded in 1971 by Brookhaven National Laboratory, New York

-PDB is an important resource for research in the academic, pharmaceutical, and biotechnology sectors
Format is save in mmCIF(macromolecular Crystallograhic Information File)

The dictionary definition language (DDL) is structured in a way that data files that conform to this syntax can be readily loaded into a database

Software tools...

pdb-extract
ADIT
PDB Validation Suite

Data Query....

Compound Information	Myoglobin,Lysozyme
Number of chains	1-5
Secondary structure content	Present of alpha min 80%

Example of protein data bank content.

NAME	EXPLANATION
Structure of ClpP in complex with ADEP1	Clp-family proteins are prototypes for studying the mechanism of ATP-dependent proteases because the proteolytic activity of the ClpP core is tightly regulated by activating Clp-ATPases. The structures of Bacillus subtilis ClpP alone and in complex with ADEP1 and ADEP2.

NAME	EXPLANATION
TRYPSIN INHIBITOR (T1) FROM NICOTIANA ALATA	The three-dimensional structures of a series of 6-kDa trypsin inhibitors isolated from the stigma of the ornamental tobacco Nicotiana alata have been determined by 1H NMR spectroscopy combined with simulated annealing calculations

What is XML?

XML stands for EXtensible Markup Language
XML is a markup language much like HTML
XML was designed to carry data
XML tags are not predefined. You must define your own tags
END tags is crucial
XML is designed to be self-descriptive

The Difference Between XML and HTML

XML is not a replacement for HTML.

XML and HTML were designed with different goals:

XML/th>	HTML/th>
Design to transport & store data	Design to display data
"Focus on what the data about"	"Focus on how data looks"
Carrying information	Display information

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:

<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.

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.

XML is Not a Replacement for HTML

XML is a complement to HTML.
It is important to understand that XML is not a replacement for HTML. In most web applications, XML is used to transport data, while HTML is used to format and display the data.
My best description of XML is this:
XML is a software- and hardware-independent tool for carrying information.

XML is Everywhere

XML is now as important for the Web as HTML was to the foundation of the Web.
XML is the most common tool for data transmissions between all sorts of applications.

HTML

What is HTML?

HTML is a language for describing web pages.

HTML stands for Hyper Text Markup Language
HTML is a markup language
A markup language is a set of markup tags
The tags describe document content
HTML documents contain HTML tags and plain text
HTML documents are also called web pages

HTML code example:

<!DOCTYPE html>

<html>

<body>

<h1>My First Heading</h1>

<p>My first paragraph.</p>

</body>

</html>

Web Browsers

The purpose of a web browser (such as Google Chrome, Internet Explorer, Firefox, Safari) is to read HTML documents and display them as web pages. The browser does not display the HTML tags, but uses the tags to interpret the content of the page:

HTML Page Structure

Below is a visualization of an HTML page structure:

<html>

<body>

<h1>This a Heading</h1>

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

<p>This is another paragraph.</p>

</body>

</html>

HTML Versions

Since the early days of the web, there have been many versions of HTML:

Version	Year
HTML	1991
HTML+	1993
HTML 2.0	1995
HTML 3.2	1997
HTML 4.01	1999
XHTML 1.0	2000
HTML 5	2012
XHTML 5	2013

SMILES

SMILES as a simple yet comprehensive chemical language in which molecules and reactions can be specified using ASCII characters representing atom and bond symbols. SMILES contains the same information as is found in an extended connection table but with several advantages. A SMILES string is human understandable, very compact, and if canonicalized represents a unique string that can be used as a universal identifier for a specific chemical structure. In addition, a chemically correct and comprehensible depiction can be made from any SMILES string symbolizing either a molecule or reaction.

Some simple SMILES examples:

Ethanol CCO

Acetic acid CC(=O)O

Cyclohexane C1CCCCC1

Pyridine c1cnccc1

Trans-2-butene C/C=C/C

L-alanine N[C@@H](C)C(=O)O

Sodium chloride [Na+].[Cl-]

Displacement reaction C=CCBr>>C=CCI

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⁺ SO4^2-	[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

ChemSketch

ACD/ChemSketch is the intelligent,interactive all-purpose chemical drawing and graphics package from ACD/Labs developed to assist chemists quickly and easily draw molecular structures, reactions, and schematic diagrams, calculate chemical properties, and design professional reports and presentations.

Features	Descriptions
Draw	structures in 2D and 3D, reactions and rection schemes
Generate	structures from InChl and SMILES strings, IUPAC systematic names for molecules of up to 50 atoms entry rings structures
Search	search logP for industrial structures, structures in the built-in dictionary of over 165 000 systematic, trivial, and trade names

Below are some images as example:

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