PDB

Bismillahirrahmanirrahim...

Assalamualaikum dear readers!

Alhamdulillah, we have finished our last quiz for this semester and it is pretty terrible for us. But, it doesn't mean we will fail this subject. We will prove that nothing is impossible, the word impossible itself say that "I'm-possible".

So today, we will explain to you about something unrelated to our course but useful as it is applicable in our daily lives.

PROTEIN DATA BANK

A repository for three-dimensional biological macro-molecular structure, that is submitted by biologists and biochemists from around the world such as proteins and nucleic acids. It is obtained by X-ray crystallography (80%) or NMR spectroscopy (16%). 

The PDB is a key resource in areas of structural biology such as structural genomics.

HISTORY

It is founded in 1971 by Brookhaven National Laboratory, New York. The first set of data were entered on punched cards but later magnetic tapes. It is transferred to the Research Collaborators for Structural Bioinformatics (RCSB) in 1998.  

mmCIF

Before mmCIF was evolved in the late 1990's to contain the coordinates and related information, PDB file format was used. It conforms to well-documented standards and facilitates automated data management. Its dictionary contains 2500 definitions for terms used to describe the crystallographic experiment. 

mmCIF is an abbreviation of macro-molecular Crystallographic Information File. 

EXAMPLES OF PROTEINS

Taka Amylase

Assembly

Ribbon

Characteristics	Number
Chains	6
Groups	1434 (3)
Atoms	11070 (3)
Bonds	21
Helices	27
Strands	60
Turns	0
Bonds	12208

Trypsinogen

Ribbon

Characteristics	Number
Chains	0
Groups	222
Atoms	1621
Bonds	6
Helices	3
Strands	13
Turns	0
Bonds	1654

Sucrase-isomaltase

Ribbon

Characteristics	Number
Chains	8
Groups	3480 (19)
Atoms	27420 (248)
Bonds	282
Helices	87
Strands	216
Turns	0
Bonds	28485

Lipase

Assembly

Ribbon

Characteristics	Number
Chains	8
Groups	1272 (4)
Atoms	9316 (4)
Bonds	20
Helices	48
Strands	56
Turns	0
Bonds	9484

Pepsinogen

Ribbo

Assembly

Characteristics	Number
Chains	2
Groups	369 (238)
Atoms	2784 (247)
Bonds	14
Helices	16
Strands	18
Turns	0
Bonds	2857

Thank you for lending your time to read this post. Hope you enjoy it. XOXO 

SMILES :)

Bismillahirrahmanirrahim

Assalamualaikum dear brothers and sisters!

It has been a tiring week since the final examination is around the corner. But giving up is not in our lives' dictionary. 

Today's post, maybe last maybe not is about SMILES.

SMILES

An abbreviation of Simplified Molecular-Input Line-Entry System. A specification in form of a line notation for describing the structure of chemical structures using short ASCII strings. It can be imported by most molecule editors for conversion back into two-dimensional or three-dimensional models of the molecules. It was initiated by the author David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in 1980s. (wikipedia)

Canonical SMILES

The SMILES format is a linear text format which can describe the connectivity and chirality of a molecule. Canonical SMILES gives a single 'canonical' form for any particular molecule. 

Isomeric SMILES

The version of the SMILES specification that includes extensions to support the specification of isotopes, chirality and configuration about double bonds.

Applications of SMILES

No.	Applications	Explanations and Examples
1	SMILES Bond	SINGLE ( - ) DOUBLE ( = ) TRIPLE (# ) AROMATIC ( * ) For example, Ethene C=CChloroethene ClC=C 1,1-Dichloroethene ClC(Cl)=C cis-1,2-Dichloroethene ClC=CCl Trichloroethene ClC(Cl)=CCl Perchloroethene ClC(Cl)=C(Cl)Cl ,  for cyclohexane and dioxane can be written as C1CCCCC1 and O1CCOCC1
2	SMILES Aromaticity	Aromatic C, O, S and N atoms are shown in their lower case 'c', 'o', 's' and 'n' respectively. Benzene,pyridine and furan can be represented respectively by the SMILES c1ccccc1, n1ccccc1 and o1cccc1. Bonds between aromatic atoms are, by default, aromatic although these can be specified explicitly using the ':' symbol. Aromatic atoms can be singly bonded to each other and biphenyl can be represented by c1ccccc1-c2ccccc2. Aromatic nitrogen bonded to hydrogen, as found in pyrrolemust be represented as [nH] and imidazole is written in SMILES notation as n1c[nH]cc1. Fluorenone
3	SMILES Isotopes	Isotopes are specified with a number equal to the integer isotopic mass preceding the atomic symbol. Benzene in which one atom is carbon-14 is written as [14c]1ccccc1 and deuterochloroformis [2H]C(Cl)(Cl)Cl.
4	Smiles Branches	Represented by enclosure in parentheses Can be nested or stacked Examples: CC(O)CC is 2-Butanol OCC(C)C is iso-Butanol OC(C)(C)C is tert-Butanol A branch cannot begin a SMILES notation A branch cannot immediately follow a double- or triple-bond symbol Example: C=(CC)C is invalid, but C(=CC)C or C(CC)=C are valid SMILES
5	SMILES Symbols	String of alphanumeric characters and certain punctuation symbols Terminates at the first space encountered when read left to right The ORGANIC SUBSET: B, C, N, O, P, S, F, Cl, Br, I
6	Other SMILES Atoms	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
7	SMILES Charges	Specify attached hydrogens and charges in square brackets Number of attached hydrogens is the symbol H followed by optional digit Examples: [H+] proton [OH-] hydroxyl anion [OH3+] hydronium cation [Fe++] iron(II) cation
8	SMILES Cyclic Structures	Break one single or one aromatic bond in each ring Number in any order –.Designate ring-breaking atoms by the same digit following the atomic symbol. 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 Atom can be associated w. 2 consecutive numbers, e.g., Napthalene: c12ccccc1cccc2
9	SMILES Conventions	Avoid two consecutive left parentheses if possible. Strive for the fewest number of possible branches Tautomeric bonds are not designated; enter the appropriate form
10	SMILES Fragments	Nitro N(=O)(=O), Nitrate ON(=O)(=O), Nitrite ON(=O), Sulfonic acid S(=O)(=O)O, Cyanide/Nitrile C#N, Azide N=N#N, Azido N+=N-
11	SMILES Metals	[Al] [As] [Au] [Be] [Bi] [Cd] [Ca] [Fe] [Hg] [K] [Li] [Mg] Na] [Ni] [Pt] [Sb] [Sn] [Zn] [Zr]

Examples of Molecular Structure and SMILES Notations

	c1ccccc1 C1=CC=CC=C1	benzene
	c1ccc2CCCc2c1 C1=CC=CC(CCC2)=C12	indane
	c1occc1 C1OC=CC=C1	furan
	c1ccc1 C1=CC=C1	cyclobutadiene

We hope this information is suffice for you to refer. Thanks for lending your time here. 

Have a good day, XOXO. 

XML better than HTML?

Bismillahirrahmanirrahim..

Assalamualaikum dear readers!

How are you guys? Feeling better after reading the Internet's post? Feeling thankful for those whose created the Internet? I'm pretty sure you will, though there are bad sides of it. Hehehe

In this post, we will explain about XML. 

XML

XML stand for Extensible Markup Language. It is a markup language that defines a set of rules for encoding documents in a format which is both human-readable and machine-readable. It was designed to describe data and focus what data is. It is also a software-hardware independent tools for carrying information. XML is different from HTML.

XML	HTML
Markup language defines a set of rules for encoding document that can be read by both humans and machines. Designed with focus on storing and transporting data.            Carrying information            Designed to transport and store data with focus on what data is	Markup language for displaying web pages in a web browser. Designed to display data with focus on how the data looks.            Displaying information            Designed to display data with focus on how data looks.

XML Tree

The XML documents form a tree structure that starts at "the root" and branch to "the leaves". XML documents must contain a root element. This element is "the parent" of all other elements.

ROOT à BRANCHES à LEAVES 

Below is the example of XML tree. 

XML Tree

<bookstore>
  <book category="COOKING">
    <title lang="en">Everyday Italian</title>
    <author>Giada De Laurentiis</author>
    <year>2005</year>
    <price>30.00</price>
  </book>
  <book category="CHILDREN">
    <title lang="en">Harry Potter</title>
    <author>J K. Rowling</author>
    <year>2005</year>
    <price>29.99</price>
  </book>
  <book category="WEB">
    <title lang="en">Learning XML</title>
    <author>Erik T. Ray</author>
    <year>2003</year>
    <price>39.95</price>
  </book>
</bookstore>

XML Rules

• XML Syntax Rules
• All XML elements must have a closing tag
• <p>This is paragraph</>
• XML Tags are case sensitive
• The tag<Letter> is different from the tag<letter>
• <Message>This is incorrect</message>
• <message>This is correct<message>
• XML elements must be properly nested
• All elements must be properly nested within each other.
• <b><i>This text is bold and italic. True</i></b>
• <b><i>This text is bold and italic. False</b></i>
• XML naming elements
• Names can contain letters, numbers and other characters.
• Names cannot start with a number.
• Names cannot start with the letters like letters xml, XML or etc. 

Before you learn XML, you should have a basic understanding of HTML and Javascript. Thank you for lending your time to read this post. 

Have a good day! XOXO