WHAT IS PROTEIN DATA BANK?

The Protein Data Bank (PDB) is a repository for the three-dimensional structural data of large biological molecules.The data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologist and biochemist 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 archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies.

ORGANISMS	NUMBER OF MOLECULES
Homo sapiens	13
Candida albicans	4
Gallus gallus	2
Sus scrofa	1

There are 5 proteins that we are able to find out and each of these proteins has many examples (only one shown):

• HtrA: Serine protease HTRA1
• Subtilisin: SUBTILISIN BPN'
• Collagenase
• Aminopeptidase
• Carboxypeptidase

Serine protease HTRA1

This figure shows the details of the protein above;

SUBTILISIN BPN'

This figure shows the details of the protein above;

Aminopeptidase

Detail information of this protein can be known from the figure below.

Carboxypeptidase

Detail information of this protein can be known from the figure below.

                                                                                          Collagenase

Detail information of this protein can be known from the figure below.

SMILE~

What is 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. You do not need to worry about ambiguous representations because the software will automatically reorder your entry into a unique SMILES string when necessary.

SMILES was developed through funding from the U.S. Environmental Protection Agency, Mid-Continent Ecology Division-Duluth, (MED-Duluth) Duluth, MN to the Medicinal Chemistry Project at Pomona College, Claremont, CA and the Computer Sciences Corporation, Duluth, MN. Several publications discuss SMILES in more detail, including Anderson et al. 1987, Weininger 1988, Weininger et al. 1989, and Hunter et al., 1987.

SMILES has five basic syntax rules which must be observed. If basic rules of chemistry are not followed in SMILES entry, the system will warn the user and ask that the structure be edited or reentered. For example, if the user places too many bonds on an atom, a SMILES warning will appear that the structure is impossible. The rules are described below and some examples are provided. The rules below allow for the representation of a two-dimensional structure of a chemical. For the ASTER system, a two-dimensional depiction is adequate. Other rules are available for chemicals that are structural isomers, but will not be discussed in this basic tutorial.

Rule One: Atoms and Bonds

SMILES supports all elements in the periodic table. An atom is represented using its respective atomic symbol. Upper case letters refer to non-aromatic atoms; lower case letters refer to aromatic atoms. If the atomic symbol has more than one letter the second letter must be lower case.

Bonds are denoted as shown below:

-	Single bond
=	Double bond
#	Triple bond
*	Aromatic bond
.	Disconnected structures

Single bonds are the default and therefore need not be entered. For example, 'CC' would mean that there is a non-aromatic carbon attached to another non-aromatic carbon by a single bond, and the computer would identify the structure as the chemical ethane. It is also assumed that the bond between two lower case atom symbols is aromatic. A blank terminates the SMILES string.

Rule Two: Simple Chains

By combining atomic symbols and bond symbols simple chain structures can be represented. The structures that are entered using SMILES are hydrogen-suppressed, that is to say that the molecules are represented without hydrogens. The SMILES software understands the number of possible connections that an atom can have. If enough bonds are not identified by the user through SMILES notation, the system will automatically assume that the other connections are satisfied by hydrogen bonds.

Some examples:

MOLECULAR FORMULA	MOLECULAR NAME
CC(O)C	2-Propanol
CC(=O)C	2-Propanone
CC(CC)C	2-Methylbutane
CC(C)CC(=O)	2-Methylbutanal
c1c(N(=O)=O)cccc1	Nitrobenzene
CC(C)(C)CC	2,2-Dimethylbutane

The user can explicitly identify the hydrogen bonds, but if one hydrogen bond is identified in the string, the SMILES interpreter will assume that the user has identified all hydrogens for that molecule.

HC(H)=C(H)(H)

Ethene

Because SMILES allows entry of all elements in the periodic table, and also utilizes hydrogen suppression, the user should be aware of chemicals with two letters that could be misinterpreted by the computer. For example, 'Sc' could be interpreted as a sulfur atom connected to an aromatic carbon by a single bond, or it could be the symbol for scandium. The SMILES interpreter gives priority to the interpretation of a single bond connecting a sulfur atom and an aromatic carbon. To identify scandium the user should enter [Sc].

Rule Three: Branches

A branch from a chain is specified by placing the SMILES symbol(s) for the branch between parenthesis. The string in parentheses is placed directly after the symbol for the atom to which it is connected. If it is connected by a double or triple bond, the bond symbol immediately follows the left parenthesis. 

Some examples:

CARBON BOND	MOLECULAR FORMULA	MOLECULAR NAME
CC	CH3CH3	Ethane
C=C	CH2CH2	Ethene
CBr	CH3Br	Bromomethane
C#N	C=N	Hydrocyanic acid
Na.Cl	NaCl	Sodium chloride

Rule Four: Rings

SMILES allows a user to identify ring structures by using numbers to identify the opening and closing ring atom. For example, in C1CCCCC1, the first carbon has a number '1' which connects by a single bond with the last carbon which also has a number '1'. The resulting structure is cyclohexane. Chemicals that have multiple rings may be identified by using different numbers for each ring. If a double, single, or aromatic bond is used for the ring closure, the bond symbol is placed before the ring closure number. 

Some examples:

MOLECULAR FORMULA	MOLECULAR NAME
C=1CCCCC1	Cyclohexene
C*1*C*C*C*C*C1
c1ccccc1	Benzene
C1OC1CC	Ethyloxirane
c1cc2ccccc2cc1	Naphthalene

Rule Five: Charged Atoms

Charges on an atom can be used to override the knowledge regarding valence that is built into SMILES software. The format for identifying a charged atom consists of the atom followed by brackets which enclose the charge on the atom. The number of charges may be explicitly stated ({-1}) or not ({-}). 

For example:

MOLECULAR FORMULA	OBSERVATION
CCC(=O)O{-1}	Ionized form of propanoic acid
CCC(=O)O{-}	Ionized form of propanoic acid
c1ccccn{+1}1CC(=O)O	1-Carboxylmethyl pyridinium

All of this were taken from this website. 

Chem Sketch Software.

Introduction:

       Chem Sketch is an alternative tool for scientist, teachers and student to computerize their chemistry's diagrams. Drawing chemical bonds and atoms is the basic activity in ACD/ChemSketch. For that reason, be sure to be in the structure mode.

The Draw Normal tool is the default tool when the program is started.

eg:

the draw tool,

the cabon element too. we can also find many other elements tool such as N, H, O and more.

NO.	TYPES OF CHEMSKETCH DRAWING
1	Energy of Reaction Diagram
2	Different Kinds of Orbital
3	Vacuum Distillation Apparatus
4	Two-chain DNA Strand
5	Lipids and Micelles

        Another interesting part is, on the Atoms toolbar,we can find the Periodic Table of Elements dialog box:

  In short, there so many interactive tools to make it easy for us to deal with our chemistry tasks.

     For this post especially, we are going to briefly explain the use of this software  to sketch: diagrams of the energy of reaction, various types of orbitals vacuum, distillation apparatus, a two-chain DNA strand, and lipids and micelles .

Drawing Energy Reaction Diagram.
 Let me show you how to make Energy Reaction Diagrams.

It looks hard to make it, but after several trials and errors, you will be satisfied with the result though.

                                

There are 3 sections in making this diagram.

A. Drawing a Curve

This section describes how to draw a curve.

1. Switch to the Draw mode by clicking on the General toolbar.

2. Form the File menu, choose New to start a new document.

3. On the Drawing toolbar, click Polyline .

4. Drag horizontally to the right from the starting point of the curve to stretch the control line.

5. Release the mouse button.

6. Move the mouse up to draw the first segment of the curve.

7. Drag horizontally to the right to stretch the control lines. By changing the length of the control lines you can     modify the curve segment.

8. Release the mouse button.

9. Move the mouse down to draw the next segment

10. Repeat the above steps to draw the next two segments.

11. Right-click to finish drawing the curve.

B. Modifying a Curve

The first time you draw with the Polyline tool you might have some trouble getting the curve to turn out the way you want. 

1. If the curve is not already selected, click Select/Move/Resize and then click the curve.

2. On the Editing toolbar, click Edit Nodes . This will show all the nodes of the polyline that can be modified:

3. Click the third node, and you will see the node selected and the control lines appear:

4. Drag the control lines, then select and modify the other nodes until the curve looks as you like.

C. Drawing the X and Y axes

To accomplish drawing of a reaction diagram, the axes are required. Make sure that the Line and Arrow tools are active.

1. From the Tools menu, choose Arrow Style Panel. On the Arrow panel that appears, from the Arrow             Type drop-down list , choose the one-way arrow .

2. From the Options menu, choose Snap on Grid and/or Show Grid to make your drawing easier.

3. Click at the origin of coordinates and drag the mouse up vertically to draw the Y-axis.

4. Click at the origin of coordinates and drag the mouse horizontally to the right to draw the X-axis.

5. Add inscriptions Energy and Reaction Coordinate using the Text and Rotate 90°

Done!! Easy, huh?

Good luck on trying them!

Drawing Different Kinds of Orbitals

There are three different types of orbital. To start drawing, choose Draw button and Polygon icon first. Then you can adjust the structure by dragging the cursor approppriately.

1) p-orbital

To draw this, the initial steps are as follows:

2) d-orbital

To draw this, the initial steps are as follows:

3) pi-type orbital

To draw this, the initial steps are as follows:

Drawing Vacuum Distillation Apparatus

To draw this structure, all the apparatus can be taken from Template Window (on the Menu Bar)>Template List> Lab Kit.

Then organize the arrangement as we desired. The steps are as follows:

To insert the caption box like this;

 The steps are as follows:

DNA Sketch

to make a DNA sketch, 

1. Make sure you are in the draw mood and clear the screen, then switch to and click Polyline
2. then, drag it in this diagram direction.
   
3. to copy the object hold down CTRL+SHIFT, drag it down
4. after copying it, connect the lines and edit the nodes

     5.Make a copy of the obtained segment by dragging it with CTRL+SHIFT, then flip left to right  and send to             back 

    6.Select both segments by dragging or clicking while holding down SHIFT and make a copy (CTRL+drag).              Correct the position using Center Horizontally tool

    7.Double-click on any of them to open the Objects panel. On the Fill tab specify the following settings:        

    8. after clicking apply, it will become somewhere like this,

       

   9.do it again for the segment that has not been fill yet

  10.Select the whole spiral by dragging the selection rectangle so that it includes all the spiral segments and make a copy of it by dragging while holding down CTRL. Click Flip Left to Right and then FlipToptoBottom:

  11.Select the segments marked with bullets in the picture below by clicking while holding down SHIFT, and then click Send to Back

  12. lastly,Select all the segments and group them.

drawing lipids and micelles.

These are the simple steps in drawing the lipids structures. 

first of all, be sure to change to the draw mode, .

Next, Click Ellipse .  Drag in the workspace while holding down SHIFT to draw a circle.

Click on the black color of the Color Palette to fill the circle.  Note that you may use any colour you wish to.

 After that, click Polyline tail and right-click to finish drawing. 

the method of drawing the zigzag correctly.

To easily draw the symmetric zigzag line, you may previously choose the Snap on Grid and/or ShowGrid command (Options menu).

for any further details do refer to this website:http://www.acdlabs.com/products/draw_nom/draw/chemsketch/