SMILES and PDB (Protein Data Bank)

Assalamualaikum and hello there !

Do you know about SMILE and PDB ? No ? I would like to tell you a little. Keep on reading :)

First of all, we go to the SMILES. SMILES (Simplified Molecular Input Line Entry System) is a chemical notation that allows a user to represent a chemical structure in a way that can be used by the computer. SMILES is an easily learned and flexible notation. The SMILES notation requires that you learn a handful of rules. 

SMILES on ChemSketch

If you still remember our previous post telling about ChemSketch, this SMILES is one of the features of that software. SMILES would help you to create the professional reports that working with structure.

Chemical Notation

Here we share with you the tutorial of how to make SMILES by using ChemSketch : Quick ChemSketch Tutorial

SMILES Structure Notation :

Type	Structure Drawing	Explanation
Atoms	[B] [OH3+]  C  N	Element Boron Hydronium ion Methane Ammonia
Bonds	CC or C-C or [CH3]-[CH3] CC#C	Ethane Propyne
Branches	CC(C)C(=O)OC CCN(CC)CC	Methyl isobutyrate Triethylamine
Rings	C1CCCC1 CC1CCC1 c1ccccc1	Cyclopentane Methylcyclobutane Benzene

PDB (Protein Data Bank)

Do you know what is this?

PDB is a repository for 3-D biological macromolecular structure.Currently it holds more than 100,000 released structure.The data is acsessable to the public.To take a look at the data you can refer to this :    PDB-Protein Data Bank.

                                                            

                                                                  Ebola virus

All the data are obtained by two methods.First, by X-Ray crytallography and secondly by NMR spectroscopy.

Exp. Method	Proteins	Nucleic Acids
X-Ray	86173	1574
NMR	9326	1096