S.M.I.L.E.S

SMILES~

Smiles is sedekah~~

BUT, this S.M.I.L.E.S is about the Simplified Molecular-Input Line-Entry System or SMILES is a specification in form of a line notation for describing the structure of chemicalmolecules using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings orthree-dimensional models of the molecules.

The original SMILES specification was initiated by the author David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s.^[1][2][3] Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo (USEPA) and Albert Leo and Corwin Hansch (Pomona College) for supporting the work, and Arthur Weininger (Pomona; Daylight CIS) and Jeremy Scofield (Cedar River Software, Renton, WA) for assistance in programming the system."^[4] The Environmental Protection Agency funded the initial project to develop SMILES.^[5][6]

It has since been modified and extended by others, most notably by Daylight Chemical Information Systems Inc. In 2007, an open standard called "OpenSMILES" was developed by the Blue Obelisk open-source chemistry community. Other 'linear' notations include theWiswesser Line Notation (WLN), ROSDAL and SLN (Tripos Inc).

In July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI; it also has a wide base of software support with extensive theoretical (e.g.,graph theory) backing.

           

                                                            SMILES BONDS

             There are 4 types of bonds:

Bonds	Symbol
Single	-
Double	=
Triple	#
Aromatic	:

example:

                                                             SMILES notation: C=C

                                                            SMILES notation: C#C

any information please refer to this link:

1-https://www.google.com/search?q=smiles&espv=210&es_sm=93&source=lnms&tbm=isch&sa=X&ei=_dOwUsOpIsjArAfEsYCQDQ&ved=0CAkQ_AUoAQ&biw=1366&bih=637

2-http://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system

Protein Data Bank

DO you know what is Protein Data Bank?

The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. (See also crystallographic database.) 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 (PDBe, PDBj, and RCSB). 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.

The polymerase chain reaction (PCR) is a biochemical technology in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.

TABLE OF MOLECULE BY RasMol.

PROTEIN TYPES	PICTURES
HtrA Molecule: Protease Do-like 8, chloroplastic Polymer: 1 Type: protein Length: 368 Chains: A, B, C EC#: 3.4.21 Fragment: UNP residues 91-448 Mutation: S204A Organism Arabidopsis thaliana Gene Names DEGP8 At5g39830 K13H13.1 UniProtKB: Protein Feature View | Search PDB | Q9LU10
SUBTILISIN Molecule: SUBTILISIN BPN' Polymer: 1 Type: protein Length: 263 Chains: A EC#: 3.4.21.62 Fragment: RESIDUES 111-181,191-382 Mutation: YES Organism Bacillus amyloliquefaciens Gene Name apr UniProtKB: Protein Feature View | Search PDB | P00782
COLLAGENASE Molecule: COLLAGENASE Polymer: 1 Type: protein Length: 230 Chains: A, B EC#: 3.4.21.49 Organism Hypoderma lineatum UniProtKB: Protein Feature View | Search PDB | P08897
CARBOXYPEPTIDASE Molecule: CARBOXYPEPTIDASE A Polymer: 1 Type: protein Length: 307 Chains: A EC#: 3.4.17.1 Organism Bos taurus Gene Names CPA1 CPA UniProtKB: Protein Feature View | Search PDB | P00730
AMINOPEPTIDASE Molecule: Aminopeptidase P; XAA-pro aminopeptidase Polymer: 1 Type: protein Length: 131 Chains: A, B Organism Streptococcus thermophilus LMG 18311 Gene Names pepP stu1742 UniProtKB: Protein Feature View | Search PDB | Q5M2R3

for more information, you all can refer to this Link:

1. http://www.rcsb.org/pdb/home/home.do 
2. http://en.wikipedia.org/wiki/Protein_Data_Bank 
3. http://en.wikipedia.org/wiki/Polymerase_chain_reaction 

ChemSketch


ChemSketch is a free chemistry drawing tool which can be used to draw chemical structures and also to draw reactions. It lets you make molecules and structures in the most simple way on the computer. It produces IUPAC names for the structures you make. It can also show you the molecule in a 3D view and also can show you the ball and stick model of the molecule. It has inbuilt templates which has ready made molecules of sugars, amino-acids and vitamins and lots more. It gives you predicted physical data about the molecule and can be used for NMR studies too. You can even write reactions and draw structures to save them for seminars or projects or reports in the form of images. It is one of the fastest chemistry drawing applications available and the best part is its free for home and educational use. It also has simple features such as molecular weight calculation and it has ready made functional groups so that you can just add them with simple clicks. It also has the ability to check the molecule online on the pubchem database as well as the eMolecules database for the structure and produces monographs of the molecule if it finds it. A very useful software and a must to download.
The software is Free for non-commercial use but a paid version of it also exists where you get all the features.Among other features, ChemSketch has the ability to:

• Draw and view structures in 2D, or render in 3D to view from any angle
• Draw reactions and reaction schemes, and calculate reactant quantities
• Generate structures from InChI and SMILES strings
• Generate IUPAC systematic names for molecules of up to 50 atoms and 3 ring structures
• Predict logP for individual structures
• Search for structures in the built-in dictionary of over 165,000 systematic, trivial, and trade names  

                                                                           Image:

 

These are some advantages and disadvantages of using ChemSketch:

ADVANTAGES	DISADVANTAGES
Sketching be faster	Difficult for first learner
Smooth and not messy	Downloading the software according to internet connection.

 

 Links:

1. http://www.intellogist.com/wiki/ChemSketch
2.  http://pharmaxchange.info/press/2011/01/acdlabs-com-chemsketch/
3.  https://sites.google.com/site/kelaskoskerol32/aaachem sketch -