Simplified Molecular-Input Line-Entry System

(SMILES) 

SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions. Some examples are:

SMILES contains the same information as might be found in an extended connection table. The primary reason SMILES is more useful than a connection table is that it is a linguistic construct, rather than a computer data structure. SMILES is a true language, albeit with a simple vocabulary (atom and bond symbols) and only a few grammar rules. SMILES representations of structure can in turn be used as "words" in the vocabulary of other languages designed for storage of chemical information (information about chemicals) and chemical intelligence (information about chemistry).

Part of the power of SMILES is that unique SMILES exist. With standard SMILES, the name of a molecule is synonymous with its structure; with unique SMILES, the name is universal. Anyone in the world who uses unique SMILES to name a molecule will choose the exact same name.

Atoms are represented by their atomic symbols: this is the only required use of letters in SMILES. Each non-hydrogen atom is specified independently by its atomic symbol enclosed in square brackets, [ ]. The second letter of two-character symbols must be entered in lower case. Elements in the "organic subset" B, C, N, O, P, S, F, Cl, Br, and I may be written without brackets if the number of attached hydrogens conforms to the lowest normal valence consistent with explicit bonds. 

Branches are specified by enclosing them in parentheses, and can be nested or stacked. In all cases, the implicit connection to a parenthesized expression (a "branch") is to the left. 

Cyclic structures are represented by breaking one bond in each ring. The bonds are numbered in any order, designating ring opening (or ring closure) bonds by a digit immediately following the atomic symbol at each ring closure. 

For further information, click SMILES

PROTEIN DATA BANK

     The Protein Data Bank (PDB) is a repository for the 3-D structural data of large biological molecules, such as protein, nucleic acids and viruses. All data are available to the public.It can be obtained by X-Ray crystallography (80%) or NMR spectroscopy (16%). It is submitted by biologists and biochemists from all around the world.

     PDB is an important resource for research in the

academic, pharmaceutical, and biotechnology

sectors.

Information required includes:-

   – Coordinates of all the atoms

   – Chemical description of the various molecules

       in the crystal

   – Experimental information about the structure

   – Structural description of the biological molecule

First, if you want to make 3-D structure for protein, you must go to Protein Data Bank and type the name of protein that you want in the box provided and click the arrow pointed in the picture below.

Then, after you get the structure that you want, download it. 

To view and edit the structure, you must download RasMol.

Happy editing your picture!!! ^_^ 

This is our 1st attempt in editing protein stuctures with RasMol

Enjoy The Picture~~~

NAME: ClpP (2FZS)
DISPLAY: CARTOONS
COLOUR: USER

NAME: DegP (1KY9)
DISPLAY: BALL AND STICK
COLOUR: STRUCTURE

NAME: THERMOLYSIN (3FLF)
DISPLAY: STICK
COLOUR: TEMPERATURE

NAME: TRYPSIN (1TIE)
DISPLAY: CARTOON
COLOUR: TEMPERATURE

Name	ClpP	DegP	Thermolysin	Trypsin
Type	2FZS	1KY9	3FLF	1TIE
Molecule	TP-dependent Clp protease proteolytic subunit	PROTEASE DO	Thermolysin	ERYTHRINA TRYPSIN INHIBITOR
Length	193	448	316	172
Organism	Escherichia coli	Escherichia coli	Bacillus thermoproteolyticus	Erythrina caffra
Link	http://www.rcsb.org/pdb/explore/explore.do?structureId=2FZS	http://www.rcsb.org/pdb/explore/explore.do?structureId=1KY9	http://www.rcsb.org/pdb/explore/explore.do?structureId=3FLF	http://www.rcsb.org/pdb/explore/explore.do?structureId=1TIE