THE PROTEIN DATABANK (PDB)

INTRODUCTION

      The Protein Data Bank (PDB) was created at Brookhaven National Laboratories (BNL) (1) in 1971 as an achieve for biological macromolecular crystal structures. In the beginning the achive had seven structures, and with a handful annually more were deposited. In the 1980s the number of deposited structures began to rise dramatically. This was due to the developed technology for all elements of the crustallographic process, the add-on of structures influenced by nuclear magnetic resonance (NMR) methods, and changes in the community views about data sharing.

      In October 1998, the management of the PDB became the responsibility of the Research Collaboratory for Structural Bioinformatics (RCSB). In general, the goal of the RCSB is to establish a reference based on the most sophisticated technology that alleviate the use and analysis of structural data and hence creates a resource for the research of biology.

The printscreen of The Protein Data Bank (PDB) website.

http://www.rcsb.org/pdb/explore/explore.do?structureId=3Q6R

Here we attached some molecules that is deposited in the Protein Data Bank (PDB)

Molecule Name	LIPASE
Classification	LIPASE
Brookhaven code	1GT6
Number of chains	6
Number of groups	538(171)
Number of atoms	4140(209)
Number of bonds	4280

Molecule Name	NEPRILYSIN
Classification	HYDROLASE
Brookhaven code	1R1H
Number of chains	2
Number of groups	696(300)
Number of atoms	5595(367)
Number of bonds	5787

Molecule Name	PROBABLE PROTEASE HTPX HOMOLO
Classification	HYDROLASE
Brookhaven code	3CQB
Number of chains	6
Number of groups	190(217)
Number of atoms	1429(343)
Number of bonds	1619

Molecule Name	ATP-DEPENDENT PROTEASE LA 1
Classification	HYDROLASE
Brookhaven code	3M65
Number of chains	4
Number of groups	408(36)
Number of atoms	3290(36)
Number of bonds	3336

Molecule Name	CYCLOPHILIN
Classification	ISOMERASE(PEPTIDYL-PROLYL CIS-TRANS)
Brookhaven code	1CLH
Number of chains	-
Number of groups	166
Number of atoms	2535
Number of bonds	2607

Molecule Name	CAPSID PROTEIN
Classification	VIRAL PROTEIN
Brookhaven code	3Q6R
Number of chains	6
Number of groups	620(990)
Number of atoms	4826(1067)
Number of bonds	5087

CONCLUSION

      We are thankful as we were blessed with this opportunity to learn this Protein Data Bank (PDB). Even though we are not major in this biological course, but we are so excited to know this application of RasWin which can portray the structural  molecular.   

IP Address

Introduction

IP address. What is IP address? Is it just merely an address? Of course not. IP address is short for Internet Protocol (IP) address. It is an identifier for a computer or device on a TCP/IP network. It is a numerical label assigned to each device (e.g., computer, printer) participating in a computer network that uses the Internet Protocol for communication.

The format of an IP address is a 32-bit numeric address written as four numbers separated by periods. Each number can be zero to 255. For example, 1.160.10.240 could be an IP address. For your information, you can view your IP address by clicking this link, http://www.myipaddress.com/show-my-ip-address/ or you can check by yourself by using your network connections. See image below

IP Tools	Explanation
IP Address Tools	The following IP address related tools are provided to our users free of charge. They can be used to help trace or track an IP address.
IP Location, Map, and Details	This tool provides details about an IP address. It's estimated physical location (country, state, and city) and a map.
Trace Email Source	This tool helps to determine the source IP address of an email based of the headers of the email. Also displays the estimated location on a map.
Visual Traceroute	This tool provides a mapped graphical representation of a traceroute from our server to the requested IP address.
Blacklist Check	This tool will check to see if your IP address is listed with more than 100 DNSbl's as a machine that mail should not be accepted from.
IP to Hostname Lookup	This tool provides the hostname of an IP address. (ie 192.168.1.1)
Hostname to IP Lookup	This tool provides the IP address of a hostname (ie www.yahoo.com)
Advanced Proxy Check	If you are using a proxy server use this tool to check and see if any information is being exposed.

XML

INTRODUCTION

Xml is the Extancible Markup Language. It is a markup language that defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. It is define in the XML 1.0 Specification produced by W3C and several other related specifications. XML emphasize simplicity, generality as well as usability over the internet.XML was designed to transport and store data.
XML tags are not predefined. You must define your own tags.

This link shows introduction to XML: http://www.youtube.com/watch?v=Q0k5ySZGPBc

Example of XML Document.

Rule	Explaination	Example
Syntax Rule	All XML elements must have a closing tag.	<p>This is a paragtaph</p>
Tags	XML tags are case sensitive.	<message>This is correct</message>
Properly Nested	In XML, all elememts must be properly  nested within each other.	<b><i>This text is bold and italic</i></b>
Root Element	XML documents must contain one element that is the parent of all other elements. This element is called the root element.	<root>    <child>      <subchild>...</subchild>    </child>  </root>
Attributes Values	In XML the attribute value must always be quoted.	<note date="26/11/2013">      <to>Mdm. Noraslinda Muhamad Bunori</to>      <from>MurNurZul</from>  </note>

HTML

Introduction

HTML is the acronym of HyperText Markup Language. This markup language is the important especially for creating worldwide web pages and other information or text to be displayed in the web browser. HTML defines the structure and layout of the web by using a variety of tags and attributes.
The basic structure is like this image;

HTML tags are mostly paired and a few tags don't have end tags. For paired tags, they begin with an opening tag and end with a matching closing tag. The pair of tags then defines the structure of the content between them. For standalone HTML tags, they don’t have end tags. They are stand-alone structure. Example

Simple Paired Tag

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

Standalone Tags	Explanation
<br>	Line-break. Starts a new line
<hr>	A horizontal rule. Puts a line across the page
<img>	An image

This link shows to us how to create basic HTML: http://www.youtube.com/watch?v=FluG2Nu8Tjg

Maple

Introduction to Maple

    Basically, according to what we have learnt Maple is a mathematical software that assists the users to solve mathematical problems. It include numeric computations, to arbitrary precision, as well symbolic computation and visualization. 

    Apart from that, Maples not only help the user to solve the algebraic equation but also plot the graphs,

differentiations,integrations and generate an annotated printout of the result. Furthermore, it also can store many information (documents,images and notes) in hierarchical structure.  

   (Example plotting a graph using Maple)

 Maple

    You can get started by referring to the tutorials that can assist you to use this software. Here we suggest you a very quick tutorial how to use the Maple.

http://www.maplesoft.com/support/training/videos/quickstart/MapleQuickStart.aspx

   In order to use the software, we have to get familiar with all the term that must be use to make the system understand to operate. For instance, when we want to use the word operand, instead of typing "operand" we have to type "op". There are many other words or operations and the terms that we have to know before getting used to Maple. As the newbies, we have Maple help to guide us. When you open the software, you go to Help menu and click Maple help.

  

Conclusion

    Overall, we found that this software is very helpful in order for us to solve some critically complicated mathematical problems.

This is the example of maple language used in the software.

Maple Language	Meaning	Example
eval	evaluate	>eval(1/2+1/3);
subs	substitute	>subs(r=3,area);
sqrt	Square root	>sqrt(2+r);
pol	polynomial	>pol:=x^2+4*x-1;
op	operand	>op(3,explist);