SMILE ALWAYS, IT IS SMILES NOTATION!!

SMILES is an acronym for Simplified Molecular Input Line Entry System. It is a chemical notation system used to represent a molecular structure by a linear string of symbols. The SMILES notation system was specifically designed for computer use by chemists. 

Atoms

Atoms are represented by their atomic symbols.

C is carbon N is nitrogen S is sulfur F is fluorine I is iodine P is phosphorus O is oxygen Cl is chlorine 

The hydrogen atom are not include in smiles notation. Hydrogen attachments are determined by the program. This greatly simplifies a SMILES notation.

Compound    Molecular Formula    SMILES Notation




Ethylene            CH2=CH2                    C=C


Propylene        CH2=CH-CH3                C=CC

2-Butene       CH3-CH=CH-CH3            CC=CC

Bond

Single bonds do not need to be shown

Compound    Molecular Formula    SMILES Notation



Propane          CH3-CH2-CH3              CCC

Butane         CH3-CH2-CH2-CH3        CCCC




Branches

Branches in molecular structures are designated by enclosures in parentheses. The examples of SMILES given in the lists above represent straight, linear compounds. When a structure contains a branch, the SMILES Notation of the structure requires that the branch be designated in enclosed parentheses. The figure below illustrates branching.






A single structure can have more than one valid SMILES notation. As an example, valid SMILES notations for the isobutyric acid structure include the following:









CC(C)C(=O)O
C(C)(C)C(=O)O
OC(=O)C(C)C
O=C(O)C(C)C




Cyclic structure






(1) Cyclic structures require numbers to indicate where the ring starts and stops. The numbers 1 through 9 are used to indicate the starting and terminating atoms.




(2) The same number is used to indicate the starting and terminating atom for each ring. The starting and terminating atom must be connected to each other!




(3) Each number that is used (1, 2, 3, etc.) must appear twice and only twice in the entire smiles notation.




(4) Numbers are entered immediately following the atoms used to indicate the starting and terminating positions.




(5) A starting or terminating atom can be associated with two consecutive numbers. For example, naphthalene can be coded as: c12ccccc1cccc2. 








Here is some example about the structures and the notation to make you more understand. 

Unbranches chain	Propane CH3-CH2-CH3 CCC Ethylene CH2=CH2 C=C 2-Butene CH3-CH=CH-CH3 CC=CC
Branches chain
Cyclic structure

If you want to further your knowledge about this SMILES Notation. You can learn from here

 That's all from us. May what have we shown to you give u a better understanding. :)

Assalammualaikum w.b.t.

IT'S CHEMSKETCH!!

          Assalammualaikum w.b.t. Here once again we've met again. This time we want to tell you about something that is really interesting and its about Chemsketch. As for us  this also our first time being introduced to Chemsketch.
     
          Chemsketch is actually about software that allow us to draw chemical substances. There is a lot of other benefits that can we have from the Chemsketch. Sometime drawing by our own hand may have difficulties in the aspect of symmetry. Then Chemsketch also helps us in drawing and viewing structure in 2D and 3D. Chemsketch generate IUPAC systematics names for molecules of up to 50 atoms and 3 ring structure. We also can draw the chemical apparatus via this applications.
     
           All the drawings are easy IF you follow the step shown in the package when you download the Chemsketch software. You can download the Chemsketch in this link .

Here I want show you the chemical substace that I managed to draw.

1. a diagram of energy reaction
2.various types of orbital
3.vacuum distillation apparatus
4.a two-chain DNA strain
5.lipids and micelles

XML

               What is XML ?XML is a markup languange that defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. is a markup language designed to give a great amount of flexibility in marking up and passing around arbitrary data. In the other word, it is called as Extensible Markup Language. XML is used to transport and to store data.

              XML is different from HTML which HTML describes the content of a Web page (mainly text and graphic images) only in terms of how it is to be displayed and interacted with. For example, the letter "p" placed within markup tags starts a new paragraph. XML describes the content in terms of what data is being described. For example, the word "phonenum" placed within markup tags could indicate that the data that followed was a phone number. The other different HTML uses <html> as the opening while XML use <note>. But don't worry because XML is simpler than HTML.

             To do the XML it must be started with <note> which I mentioned before or you can put any word that can be as a main thing. Then start to put description and the content and close the description. As example. <to>Jenny</to>. As i said the description is the one that have '< >' and the content is 'Jenny'. You can put any word that you want to describe the informations that you want to display.And at the end of it you must put </note>. But still XML does not do anything. It is just informations that wrapped in tags. You must have a piece of software to display, send or receive it.

This is an easy example about xml.:

<note>
<to>Tove</to>
<from>Jani</from>
<heading>Reminder</heading>
<body>Don't forget me this weekend!</body>
</note>

As you are getting more understand about the XML. This is the example of more complex XML.

Here are the differences between XML and HTML:

            

HTML	XML
To display data with focus on how data looks.	To transport and store data, with focus on what data is.
Case insensitive	Case sensitive
Presentation language	Neither programming language nor prensentation language.

To learn more about XML, here is the link . That's all from us which is the Imperius. Hope that you as reader can completely understands and applied it in your life. :) Assalammualaikum w.b.t.

IMPERIUS :INTO THE WORLD OF PROTEIN DATA BANK !!!!

Assalammualaikum w.b.t

Today there is another experience that we want to share with you! :)

It is all about Protein Data Bank

In this data bank we have plenty of  proteins structure which can be opened with raswin software . You can download this raswin app from this link : :raswin .before you can view the protein structures, you have todownload pdb file(text) from rscb protein bank website. Once we finish download it we can view them using the raswin app that we have download just now. So here are some protein that we can share with all of you.

Prolyl Oligopeptidase	We report the synthesis and in vitro activity of a series of novel pyrrolidinyl pyridones and pyrazinones as potent inhibitors of prolyl oligopeptidase (POP). Within this series, compound 39 was co-crystallized within the catalytic site of a human chimeric POP protein which provided a more detailed understanding of how these inhibitors interacted with the key residues within the catalytic pocket.
Thermolysin	Like all bacterial extracellular proteases thermolysin is first synthesised by the bacterium as a pre-proenzyme.[5] Thermolysin is synthesized as a pre-proenzyme consisting of a signal peptide 28 amino acids long, a pro-peptide 204 amino acids long and the mature enzyme itself 316 amino acids in length. The signal peptide acts as a signal for translocation[disambiguation needed] of pre-prothermolysin to the bacterial cytoplasmic membrane. In the periplasm pre-prothermolysin is then processed into prothermolysin by a signal peptidase. The prosequence then acts as a molecular chaperone and leads to autocleavage of the peptide bond linking pro and mature sequences. The mature protein is then secreted into the extracellular medium.[6]
Oligopeptidsae	Oligopeptidase is an enzyme that cleaves peptides but not proteins, a property that is due to its structure: the active site of this enzyme is located at the end of a narrow cavity which can only be reached by peptides. These oligopeptides, peptides, predominantely smaller than 30 amino acids in length, play essential roles as hormones, in the surveillance against pathogens, and in neurological activities. Therefore these molecules constantly need to be specifically generated and inactivated, which is the role of the oligopeptidases. Oligopeptidase is a term coined in 1979 to designate a sub-group of the endopeptidases,[1][2] which are not involved in the digestion nor in the processing of proteins like the pancreatic enzymes, proteasomes, cathepsins among many others. The prolyl-oligopeptidase or prolyl endopeptidase (POP) is a good example of how an oligopeptidase interacts with and metabolizes an oligopeptide. The peptide has first to penetrate into a 4 Å hole on the surface of the enzyme in order to reach an 8,500Å3 internal cavity, where the active site is located.[3][4] The activity of the oligopeptidase is rather selective, as experimental evidence demonstrated. They suggest that the oligopeptide should display specific structures in order to access the active site of the enzyme.[5] This peculiar mechanism of action sets the oligopeptidases at the end of the protein processing pathway, acting on specific oligopeptides, allowing them to play essential physiological and pathological roles, from microorganisms to man.
Signal Peptidase	Signal peptide peptidase A (SppA) is a membrane-bound self-compartmentalized serine protease that functions to cleave the remnant signal peptides left behind after protein secretion and cleavage by signal peptidases. SppA is found in plants, archaea and bacteria. Here, we report the first crystal structure of a Gram-positive bacterial SppA. The 2.4-Å-resolution structure of Bacillus subtilis SppA (SppA(BS)) catalytic domain reveals eight SppA(BS) molecules in the asymmetric unit, forming a dome-shaped octameric complex. The octameric state of SppA(BS) is supported by analytical size-exclusion chromatography and multi-angle light scattering analysis. Our sequence analysis, mutagenesis and activity assays are consistent with Ser147 serving as the nucleophile and Lys199 serving as the general base; however, they are located in different region of the protein, more than 29 Å apart. Only upon assembling the octamer do the serine and lysine come within close proximity, with neighboring protomers each providing one-half of the catalytic dyad, thus producing eight separate active sites within the complex, twice the number seen within Escherichia coli SppA (SppA(EC)). The SppA(BS) S1 substrate specificity pocket is deep, narrow and hydrophobic, but with a polar bottom.
Collagenase	The X-ray crystal structure of a 19 kDa active fragment of human fibroblast collagenase has been determined by the multiple isomorphous replacement method and refined at 1.56 A resolution to an R-factor of 17.4%. The current structure includes a bound hydroxamate inhibitor, 88 waters and three metal atoms (two zincs and a calcium). The overall topology of the enzyme, comprised of a five stranded beta-sheet and three alpha-helices, is similar to the thermolysin-like metalloproteinases. There are some important differences between the collagenase and thermolysin families of enzymes. The active site zinc ligands are all histidines (His-218, His-222, and His-228). The presence of a second zinc ion in a structural role is a unique feature of the matrix metalloproteinases. The binding properties of the active site cleft are more dependent on the main chain conformation of the enzyme (and substrate) compared with thermolysin. A mechanism of action for peptide cleavage similar to that of thermolysin is proposed for fibroblast collagenase.

How to use HTML code in making webpage

Assalamualaikum everyone for our second post in this blog we would like to teach you on how to use html in making a webpage. First of all we need to put the html body for our webpage. in notepad app type this words html followed by body in the new line. Make sure those words are in the "<>" sign.

Next we are going to teach you how to make a paragraph. It's simple before we begin to write down our text, just put this letter"p" and after you ended your text put this sign "/p". Just like before, dont forget to put those letters in this "<>" sign.

Actually you can learn all this through this link but fo the introduction we're just being good guys haha so below is the link for the website that can teach you a lot about html.

learn here.

There are 3 types of lists which are:

1	disc bullet
2	letters
3	nested

here is an example of more complex html which we haven't learn yet but we pretty sure it will be legend......wait for it... dary. Legendary complex html =..=

So i guess that's all, seems we have to submit this post as soon as possible or our marks will be deducted. I'm sure all of you will understand if not that means you committed in plagiarism(suddenly). Haha it just a joke ~(-.-~) so thanks for spending your precious time to read this simple blog.

OUR FIRST DAY IN IIUM KUANTAN MALAYSIA. YEAAAAYYY!!! :)

    Bismillahirrahmannirrahim. Assalammualaikum W.B.T . As you can see in the picture, that guard sent you a regard ^.^v wink wink. Actually this is my first thing that I see when I reached IIUM Kuantan. But sadly right after we register , we have to go through the orientation week :( uhukkkss!!

Our story about our first day in IIUM Kuantan was actually give us a big moment in our life. In this time we realize that IIUM will help me to achieve a better future. 

 After the registration session, we were given this mahallah called the At Tabari.Majestic name isn't it? =..+ But we only get to sleep here 2 days later after sleeping in the Sultan Haji Ahmad Shah mosque. 

 we had our qiamullail here and it was so comfortable well that is how our first day of taaruf week end ~(-.-~)

Name	Matric Number
Muhammad Ali bin Elias	1311621
Muhammad Fadhli Azhar bin Azmi	1312301
Ahmad Najib bin Mohamad	1312545
Mohamad Fakrul Ridha bin Ab Rasat	1316949

So, thats all for our first post. We're sooo tired :( hmmm
See you guys next time okay? ^_- 
Byebye <3 Assalamualaikum