~ Le Spectacles ~: 2013

Sunday, 3 November 2013

SMILES

Simplified Molecular Input Line Entry Specification

Assalamualaikum w.b.t. my fellow vicegerences of Earth! It is Wednesday and as usual we are here to equip ourselves with some IT knowledge. Today, we are going to learn a thing or two that will make you "smile". Why? We will see later on.
Surely, most of you readers are science based students and are taking organic chemistry as your required subjects. And we all know that in organic chemistry we have to deal with complicated and sometimes long and highly branched structures and formula of organic molecules. And have you ever wonder how these molecules and formulas are going to be written in computer?
Fortunately, there is a system that has made it simple. It is the Simplified Molecular Input Line Entry Specification or SMILES. SMILES is a specification for unambiguously describing 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-dimensions models of the molecules. SMILES uses atomic symbols and a set of intuitive rules. It also uses hydrogen-suppressed molecular graphs (HSMG). 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.

There are two types of SMILES:

Canonical SMILES
Isomeric SMILES

Canonical SMILES refers to the version of the SMILES specification that includes rules for ensuring that each distinct chemical molecule has a single unique SMILES representation. A common application of Canonical SMILES is for indexing and ensuring uniqueness of molecules in a database.
Isomeric SMILES refers to the version of the SMILES specification that includes extensions to support the specification of isotopes, chirality and configuration about double bonds. A notable feature of these rules is that they allow rigorous partial specification of chirality.

E.g:

trans-1,2-dibromoethene: Br/C=C/Br
cis-1,2-dibromoethene: Br/C=C\Br

Chirality indicated by the "@" symbol.

SMILES Bonds

The bonds in a molecular formula are represented with symbols such as follows:

Single*	-
Double	=
Triple	#
Aromatic	:

*can be omitted

Examples:

Molecule	SMILES representation
Ethene	C=C
Chloroethene	ClC=C
1,1-Dichloroethene	ClC(Cl)=C
cis-1,2-Dichloroethene	ClC=CCl
Trichloroethene	ClC(Cl)=CCl
Perchloroethene	ClC(Cl)=C(Cl)Cl

SMILES Branches

Branches are represented by enclosure in parentheses.
Can be nested or stacked

A branch cannot immediately follow a double or triple bond symbol. E.g:

C=(CC) is invalid, but
C(=CC)C or C(CC)-C are valid SMILES

SMILES Symbols

Are strings of alphanumeric characters and certain punctuation symbols
Termintes at the first space encountered when read left to right.
The organic subset : B, C, N, O, P, S, F, Cl, Br, I

Cyclic Structures

Aliphatic or nonaromatic carbon: C
Atom in aromatic ring : lowercase letter
Designate ring closure with pairs of matching digits, e.g:

c1ccccc1 is Benzene, whereas
C1CCCCC1 is Cyclohexane

Numbers indicate start and stop of ring.
Same number indicates start and end of the ring, entered immediately following the start/end atoms.
Only numbers 1-9 are used.
A number should appear only twice
Atm can be associated with 2 consecutive number, e.g, Naphthalene: c12ccccc1cccc2.

Here are some examples of SMILES notation for some molecules:

SMILES Charges

[H+] proton
[OH-] hydroxyl anion
[OH3+] hydronium cation
[Fe++] iron(II) cation
[NH4+] ammonium cation

When using SMILES, avoid two consecutive left parentheses if possible. Strive for the fewest number of possible branches.

Another application is SMILESCAS Database
http://esc.syrres.com/interkow/smilecas.htm
There are over 103,000 SMILES notations with input CAS Registry Number that leads to SMILES and thence to a structure search.

That's all for today's lesson and see you next time. Assalamualaikum w.b.t.
Bye!

ChemSketch

Assalamualaikumwarahmatullahiwabarakatuh .For this entry we are going to write about the chemsketch .We use this chemsketch application to create graphical objects that are often used in most of the chemistry books and many others chemistry-related references .

For your information chemsketch is a commonly used chemical drawing program for 2D and 3D structures .this program has certain additional features including calculation of molecular weight ,calculation of percentages of elements present ,IUPAC name generation and viewing in RasMol .

As in this entry we will show you the example of the objects that can be drawn using the chemsketch .there are five of them :

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

These are the images of the objects accordingly :

1. Diagram of energy reaction

2. Types of orbital

3. Vacuum distillation apparatus

4. A two-chain DNA strain

5. Lipids and Micelles

For further reference on how to use chemsketch do visit this website .

Thats all from us .Hopefully this entry will help you in your learning of chemistry .

XML

All 'bout XML

Assalamualaikum...hey, we meet again (^.^)V How are u?

Today we are going to learn about XML. You really wondering what does XML stands for right? Ok, XML stands for Extensible Markup Language which was designed solely to carry data. Wait a minute, don't get confuse between HTML and XML because HTML is all about displaying the data. In contrast to XML which is to transport and store the data.

Actually, we already been using XML since its creation. This is because it is the common tool for data transmission between applications and becoming more and more popular from the perspective of data storage and describing data. How XML separates data from HTML?

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.

With XML, data can be stored in separate XML files

This way you can concentrate on using HTML for layout and display, and be sure that changes in the underlying data will not require any changes to the HTML

With a few lines of JavaScript, you can read an external XML file and update the data content of your HTML

As example here is a note to Terry from John
<note>
<to>Terry</to>
<from>John</from>

<heading>Reminder</heading>

<body>Call me before 6 p.m.!</body>

</note>

1) XML Syntax Rules:

All XML Elements Must Have a Closing Tag

In HTML, you will often see elements that don't have a closing tag:

This is a paragraphThis is another paragraph

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

This is a paragraphThis is another paragraph

2) XML Tags are Case Sensitive:

XML elements are defined using XML tags

With XML, the tag <Letter> is different from the tag <letter>

Opening and closing tags must be written with the same case:

<Message>This is incorrect</message>

<message>This is correct</message>

3) XML Elements Must be Properly Nested

Correct: This text is bold and italic</i

Incorrect: This text is bold and italic

4) XML Documents Must Have a Root Element

XML documents must contain one element that is theparentof all other elements

<root>

<child>

<subchild>.....</subchild>

</child>

</root>

5) XML Attribute Values Must be Quoted

Correct:

<note date=12/11/2007>

<to>Terry</to>

<from>John</from>

</note>

Incorrect:

<note date="12/11/2007">

<to>Terry</to>

<from>John</from>

</note>

As conclusion, there are 2 obvious differences between XML and HTML:

XML	HTML
Designed to transport and store data, with focus on what data is	Designed to display data, with focus on how data looks
Carry information	Display information

For more info, visit this site.

Wednesday, 2 October 2013

Protein Data Bank

Assalamualaikum w.b.t

Hello again, my fellow vicegerents on Earth! Alhamdulillah, all praises to Allah that we got the chance to post this time entry as usual every Wednesday.

So, this time we are going to tell you about what we learned today in KOS1110 lecture. It is about Protein Data Bank (PDB).

First and foremost, let us introduce to you what PDB is like. All of us have at least one bank account to keep our money. The same goes with protein. In Biology world, we keep informations of many biological molecules in banks.Protein Data Bank is a repository for the 3D 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. Unfortunately, X-Ray crystallography is currently not available in IIUM Kuantan. But you can find it in Universiti Kebangsaan Malaysia.

X-Ray Crystallography

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.

PDB is an important resource for research in biological studies such as Biotechnology, Medicine and Pharmaceutical. Using the information provided by PDB helps scientists a lot to determine if certain molecules can cause cancer, or if certain combination of molecules can cure common colds, or if radiation can affect the RNA and DNA.

The PDB is updated on a weekly basis. This is the records dated on 8th September 2013:

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	77139	1481	4059	3	82682
NMR	8829	1044	193	7	10073
Electron microscopy	466	45	128	0	639
Hybrid	51	3	2	1	57
Other	150	4	6	13	173
Total:	86635	2577	4388	24	93624

So, now we will show you some examples of protein that can be found in the PDB.

1)Prolyl oligopeptidase

Classification:	Hydrolase
Structure Weight:	80842.69

Molecule:

prolyl oligopeptidase

Polymer:

Type:

protein

Length:

741

Chains:

EC#:

Organism

Novosphingobium capsulatum

Prolyl oligopeptidase

Prolyl oligopeptidase contains a peptidase domain and its catalytic triad is covered by the central tunnel of a seven-bladed beta-propeller. This domain makes the enzyme an oligopeptidase by excluding large structured peptides from the active site. The apparently rigid crystal structure does not explain how the substrate can approach the catalytic groups. Two possibilities of substrate access were investigated: either blades 1 and 7 of the propeller domain move apart, or the peptidase and/or propeller domains move to create an entry site at the domain interface. Engineering disulfide bridges to the expected oscillating structures prevented such movements, which destroyed the catalytic activity and precluded substrate binding. This indicated that concerted movements of the propeller and the peptidase domains are essential for the enzyme action.

2)Thermolysin

Classification:	Hydrolase (metalloproteinase)
Structure Weight:	34734.49

Molecule:

THERMOLYSIN

Polymer:

Type:

protein

Length:

316

Chains:

EC#:

Organism

Bacillus thermoproteolyticus

Thermolysin

The mode of binding of the irreversible thermolysin inhibitor ClCH2CO-DL-(N-OH)Leu-OCH3 [Rasnick, D., & Powers, J.C. (1978) Biochemistry 17, 4363-4369] has been determined by X-ray crystallography at a resolution of 2.3 A and the structure of the covalent complex refined to give a crystallographic residual of 17.0%. This is the first such structural study of an active-site-directed covalent complex of a zinc protease. As anticipated by Rasnick and Powers, the inhibitor alkylates Glu-143 in the thermolysin active site, and the hydroxamic acid moiety coordinates the zinc ion. The formation of the covalent complex is associated with a significant shift in a segment of the polypeptide backbone in the vicinity of the active site. This conformational adjustment appears to be necessary to relieve steric hindrance which would otherwise prevent alkylation of Glu-143. It is suggested that this steric hindrance, which occurs for thermolysin but would not be expected for carboxypeptidase A, accounts for the previously inexplicable difference in reactivity of these two metalloproteases toward N-haloacetyl amino acids. The relevance of this steric hindrance to the mechanism of catalysis is discussed. In agreement with previous results [Kester, W. R., & Matthews, B. W. (1977) Biochemistry 16, 2506-2516], it appears that steric hindrance prevents the direct attack of Glu-143 on the carbonyl carbon of an extended substrate, therefore ruling out the anhydride pathway in thermolysin-catalyzed hydrolysis of polypeptide substrates and their ester analogues.

3) Oligopeptidase

Classification:	Hydrolase
Structure Weight:	133341.53

Molecule:

Oligopeptidase

Polymer:

Type:

protein

Length:

564

Chains:

A, B

Fragment:

PEPTIDASE

Organism

Geobacillus sp. MO-1

Oligopeptidase

Pz-peptidase A, from the thermophilic bacterium Geobacillus collagenovorans MO-1, hydrolyzes a synthetic peptidesubstrate, 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-D-Arg (Pz-PLGPR), which contains a collagen-specific tripeptidesequence, -Gly-Pro-X-, but does not act on collagen proteins themselves. The mammalian enzyme, thimet oligopeptidase(TOP), which has comparable functions with bacterial Pz-peptidases but limited identity at the primary sequence level, hasrecently been subjected to x-ray crystallographic analysis; however, no crystal structure has yet been reported forcomplexes of TOP with substrate analogues. Here, we report crystallization of recombinant Pz-peptidase A in complex withtwo phosphinic peptide inhibitors (PPIs) that also function as inhibitors of TOP and determination of the crystal structure of these complexes at 1.80-2.00 Å resolution. The most striking difference between Pz-peptidase A and TOP is that there is no channel running the length of bacterial protein. Whereas the structure of TOP resembles an open bivalve, that of Pz-peptidase A is closed and globular. This suggests that collagenous peptide substrates enter the tunnel at the top gatewayof the closed Pz-peptidase A molecule, and reactant peptides are released from the bottom gateway after cleavage at theactive site located in the center of the tunnel. One of the two PPIs, PPI-2, which contains the collagen-specific sequence,helped to clarify the exquisite structure and reaction mechanism of Pz-peptidase A toward collagenous peptides. This studydescribes the mode of substrate binding and its implication for the mammalian enzymes.

4) Signal peptidase

Classification:	Hydrolase
Structure Weight:	112635.13

Molecule:

SIGNAL PEPTIDASE I

Polymer:

Type:

protein

Length:

248

Chains:

A, B, C, D

EC#:

Fragment:

CATALYTIC DOMAIN

Organism

Escherichia coli BL21(DE3)

Signal peptidase

The signal peptidase (SPase) from Escherichia coli is a membrane-bound endopeptidase with two amino-terminal transmembrane segments and a carboxy-terminal catalytic region which resides in the periplasmic space. SPase functions to release proteins that have been translocated into the inner membrane from the cell interior, by cleaving off their signal peptides. We report here the X-ray crystal structure of a catalytically active soluble fragment of E. coli SPase (SPase delta2-75). We have determined this structure at 1.9 A resolution in a complex with an inhibitor, a beta-lactam (5S,6S penem), which is covalently bound as an acyl-enzyme intermediate to the gamma-oxygen of a serine residue at position 90, demonstrating that this residue acts as the nucleophile in the hydrolytic mechanism of signal-peptide cleavage. The structure is consistent with the use by SPase of Lys 145 as a general base in the activation of the nucleophilic Ser90, explains the specificity requirement at the signal-peptide cleavage site, and reveals a large exposed hydrophobic surface which could be a site for an intimate association with the membrane. As enzymes that are essential for cell viability, bacterial SPases present a feasible antibacterial target: our determination of the SPase structure therefore provides a template for the rational design of antibiotic compounds.

5)Collagenase

Classification:	Cell Adhesion
Structure Weight:	18426.06

Molecule:

Collagenase

Polymer:

Type:

protein

Length:

Chains:

A, B

EC#:

Fragment:

PKD domain

Organism

Clostridium histolyticum

Collagenase

The crystal structure of a collagen-binding domain (CBD) with an N-terminal domain linker from Clostridium histolyticum class I collagenase was determined at 1.00 A resolution in the absence of calcium (1NQJ) and at 1.65 A resolution in the presence of calcium (1NQD). The mature enzyme is composed of four domains: a metalloprotease domain, a spacing domain and two CBDs. A 12-residue-long linker is found at the N-terminus of each CBD. In the absence of calcium, the CBD reveals a beta-sheet sandwich fold with the linker adopting an alpha-helix. The addition of calcium unwinds the linker and anchors it to the distal side of the sandwich as a new beta-strand. The conformational change of the linker upon calcium binding is confirmed by changes in the Stokes and hydrodynamic radii as measured by size exclusion chromatography and by dynamic light scattering with and without calcium. Furthermore, extensive mutagenesis of conserved surface residues and collagen-binding studies allow us to identify the collagen-binding surface of the protein and propose likely collagen-protein binding models.

So, these are the 5 examples of protein that can be found in PDB.
That's all for now. See you again. Bye
Assalamualaikum w.b.t

Thursday, 26 September 2013

HTML

Assalamualaikum w.b.t. my fellow vicegerent on Earth. It has been a while since our last post. So, how are you guys doing? We hope that Allah blessed you with health and happiness.

So, our post this time, which is our second post, we will touch about web-designing related stuffs, partiularly the HTML. Have you ever heard HTML? What is HTML? What does HTML do in web-designing. We will see the details shortly.

Definition of HTML:
HTML stands for HyperText MarkUp Language. It is the authoring language used to create documents on the World Wide Web.
HTML defines the structure and layout of a Web document by using a variety of tags and attributes. The correct structure for an HTML document starts with <HTML><Head>(enter here what document is about)<BODY> and ends with <BODY></HTML
All the information you'd like to include in your Web page fits in between the <BODY> and </BODY> tags.

Here is an example:

This is what we type in the notepad :