PROTEIN DATA BANK

Assalamualaikum... its was a long day after our kuizes. Today is our last class with madam Noraslinda. We had learn about Protein Data Bank. 

Protein Data Bank is a respiratory for three-dimensional structure 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 

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.

1. NEPRILYSIN

Neutral endopeptidase (NEP) is the major enzyme involved in the metabolic inactivation of a number of bioactive peptides including the enkephalins, substance P, endothelin, bradykinin and atrial natriuretic factor. Owing to the physiological importance of NEP in the modulation of nociceptive and pressor responses, there is considerable interest in inhibitors of this enzyme as novel analgesics and antihypertensive agents. Here, the crystal structures of the soluble extracellular domain of human NEP (residues 52-749) complexed with various potent and competitive inhibitors are described. The structures unambiguously reveal the binding mode of the different zinc-chelating groups and the subsite specificity of the enzyme. 

2. LONA

Lon ATP-dependent proteases are key components of the protein quality control systems of bacterial cells and eukaryotic organelles. 

Eubacterial Lon proteases contain an N terminal domain, an ATPase domain, and a protease domain, all in one polypeptide chain.

3. HTPX

molecular	Probable protease htpX homolog
polymer	1
chains	A,B
EC#	3.4.24
Fragment	Domain: Residues 58-161
Organism	Vibrio parahaemolyticus RIMD 2210633
Gene Names	htpX VP1118
UniProtKB	Protein Feature View | Search PDB | Q87QN1

4. PROLYL

MOLECULE	CYCLOPHILIN
POLYMER	1
TYPE	protein
LENGTH	166
CHAINS	A
EC#	5.2.1.8
ORGANISM	Escherichia coli
GENE NAMES	ppiA rot rotA b3363 JW3326

5. LEXA

MOLECULE	LEXA REPRESSOR
POLYMER	1
TYPE	protein
LENGTH	202
CHAINS	A, B
EC#	3.4.21.88
ORGANISM	Escherichia coli
GENE NAMES	lexA exrA spr tsl umuA b4043 JW4003

TCP/IP

Assalamualaikum.. Today our third class with Madam Noraslinda. We had learn about TCP/IP.

TCP/IP in commonly known as The Internet protocol suit is the nertworking model and a set of communications protocols used for the Internet and similar networks. Because its most important protocols, the Transmission Control protocol (TCP) and the Internet Protocol (IP), were the first networking protocols defined in this standard. 

How TCP/IP works?

For more information : How TCP/IP works?

Key Field for IP header

IP Header Field	Function
Source Address	The IP address of the original source of the IP datagram.
Destination Address	The IP address of the final destination of the IP datagram.
Identification	Used to identify a specific IP datagram and to identify all fragments of a specific IP datagram if fragmentation occurs.
Protocol	Informs IP at the destination host whether to pass the packet up to TCP, UDP, ICMP, or other protocols.
Checksum	A simple mathematical computation used to verify the bit-level integrity of the IP header.
Time to Live (TTL)	Designates the number of network segments on which the datagram is allowed to travel before being discarded by a router. The TTL is set by the sending host and is used to prevent packets from endlessly circulating on an IP internetwork. When forwarding an IP packet, routers are required to decrease the TTL by at least one.

XML (Extensible Markup Language)

•  markup language that defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. 
• is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications,all free open standards.

• 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.

• it is widely used for the representation of arbitrary data structures, for example in web services.

 

XML VS HTML

XML	HTML
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
is about carrying information	is about displaying information
data can be stored in separate XML files	If you need to display dynamic data in your HTML document, it will take a lot of work to edit the HTML each time the data changes

HTML

Assalamualaikum...

This is our second class with Madam Noraslinda. We learn about HTML ! what is HTML?? 

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

So... firstly, we need to open Notepad in our computer program. We need to learn how to write a code. 

This is our baby step in learning how to create a HTML.

THE INTRODUCTION 

As you can see, this is our introduction in learning HTML. After we write this code, we need to save the file as (.txt) format and save as the file as (.html) format. 

As you can see, in the red circle is the file with (.html) format.

When you open the file that contain the logo, some time the type for this file are either mozilla firefox or google chrome  or any others internet options. This is the result. 

LINK 

After that is how to link some others page on our webpage and list of our contain. 

This is a coding. 

And this is the result. This is the link to facebook. 

IMAGE

Although in this blogger.com we can easily add an image in our blog, we also learn how to put an image using HTML. I want to show you how the image will appear using HTML. This is the HTML look like. 

But, the image name must be the same as in the coding. This is how we add an image in the blog. 

We also learn how to put an moving image. 

Taraaaaa!!! The image is moving right!! Its was so easy. I want to show you the result of the coding. Wait for it.....

TABLE

Without cellpadding:

Name	Address	Phone Number	Ic	State
Fatin nabilah Binti Sidek	No,16,jalan 3B,Taman Jati,Rawang	013-2604024	931104-14-5200	Selangor

with cellpadding:

Name	Mahallah	Phone Number	State
Fatnin Nabihah	Maimunah 2	011-27000942	State
Ielya Nur Syakireen	Maimunah 2	013-3070412	Selangor
Zulaikha Ajma'ain	Maimunah 6	012-2411528	Selangor
Nashrah Fatihah	Maimunah 2	013-3479850	Selangor
Nurul Nadhirah	Tabari	010-5767645	Pahang
Nor Syifa'	Talhah 5	017-3213616	Selangor
Liyana Kassim	Maimunah 2	011-19735686	Selangor
Rabiatul Affifah	Maimunah 6	013-7689239	Kelantan
Affifah Ubaidillah	Maimunah 1	013-6823089	Terengganu
Fatin Hamizah	Maimunah 1	013-5830721	Kedah

This is the table look alike using our coding. 

That all for today. Thank you madam for teach us about HTML. 

Conclusion

There is it !!! It was not so hard to learn Maple right? we just need to know the step. The step in Maple nearly same with programming topics. But there is a little bit addition in Maple. 

In the nut shell, for those who are news in order to learn Maple, don't take it so hard. Maple will help you to do your calculation. :) 

So... happy learning Maple everybody !!!

About maple

Maple

is a commercial computer algebra system developed and sold commercially by Maplesoft, a software company also based in Waterloo, Ontario Canada The current major version is version 17 which was released in March 2013.

It was first developed in 1980 by the Symbolic Computation Group at the University of Waterloo. In 1988, Maplesoft (then known as Waterloo Maple Inc.) was founded to commercialize the technology.

Users can enter mathematics in traditional mathematical notation. Custom user interfaces can also be created. There is support for numeric computations, to arbitrary precision, as well as symbolic computation and visualization. Examples of symbolic computations are given below.

Maple Course Outline

So basically here is our course outline of our class during this Maple session

Introduction to the symbolic computation, computer algebra system and Maple software package.	Chapter 1, Textbook 1
Definitions of expression, function and equation according to Maple syntax.	Chapter 2, Textbook 1
Application of Maple in calculus; finding limit and derivative of a function and 2D graphic plots.	Chapter 3, Textbook 1
Application of Maple in calculus; solving integration and analysis of series.	Chapter 3, Textbook 1
Data structures in Maple; sequence, list, array, table and set.	Chapter 4, Textbook 2
Maple programming language; writing procedures, declaring variables and understanding for loop.	Chapter 7, Textbook 2
Maple programming language; argument type declaration, understanding the while loop and explicit return.	Chapter 7, Textbook 2