~XML~

                                                      

What is XML?

Extensible Markup Language (XML) is a set of rules for encoding documents in machine-readable form.

 XML is not a replacement for HTML.

 XML was designed to transport and store data, with focus on what data is.

XML is a software and hardware-indepedent tool for carrying information.

XML TABLE

Molecular mechanism	Semi emphirical	Ab initio
Very fast speed	Fast speed	Slow speed
Restruction parameters	Good accuracy	Very good accuracy
Very good protein modelling	Good protein modelling	Best protein modelling

XML DOCUMENT

<computational method>

   <molecular mechanism=”very fast speed”>

      <semi emphirical>fast speed</semi emphirical>

     <ab initio>slow speed</ab initio>

 </molecular mechanism>

 <molecular mechanism=”restruction parameters”>

    <semi emphirical>good accuracy</semi emphirical>

   <ab initio>very good accuracy</ab initio>

 </molecular mechanism>

 <molecular mechanism=”very good protein modelling”>

   <semi emphirical>good protein modelling</semi emphirical>

   <ab initio>best protein modelling</ab initio>

 </molecular mechanism>

</computational method>



XML TREE

PROTEIN DATA BANK

The Protein Data Bank (PDB) is a repository for the 3-D 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. 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; GO categorize structures based on genes.

                                                                PDB




The PDB database is updated weekly (on Tuesday). Likewise, the PDB Holdings List is also updated weekly. As of 21 September 2010, the breakdown of current holdings was as follows:

Experimental Method	Proteins	Nucleic Acids	Protein/Nucleic Acid complexes	Other	Total
X-ray diffraction	55480	1231	2605	17	59333
NMR	7512	925	162	7	8606
Electron microscopy	214	17	77	0	308
Hybrid	24	1	1	1	27
Other	126	4	4	13	147
Total:	63356	2178	2849	38	68421

*SMILE*

SMILE

         The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of chemical molecules using short ASCII strings

          SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules 

          SMILE Fragments

Nitrite	ON(=O)
Nitro	N(=O)(=O)
Nitrate	ON(=O)(=O)

*chemsketch*

ChemSketch

ChemSketch is designed to be used on its own for drawing chemical structures, reactions, schematic diagrams or integrated with other ACD applications and as the front end to our software. Able to import Windows Metafile, MDL MOL, CS ChemDraw, or ISIS/Sketch BIN file. Export Bitmap, TIFF, Metafile, MOL, Paintbrush, ISIS/Sketch, GIF , and ChemDraw. Fully loaded with useful pre-drawn structures including lab equipment, DNA/RNA building kit, amino acids etc. Structures can be 2D "cleaned" as well as 3D optimized using ACD's powerful algorithm. Publish a professional quality report from within ChemSketch or drag drop structures/text into MS applications i.e. MS Word.

 

Basic of Chemsketch

This is an introduction to the program ChemSketch, from ACD Labs. You can use ChemSketch to draw chemical structures, and to view them as three dimensional (3D) models.

The approach here is to show by example. I will lead you through one example in some detail, showing how to draw the structure, and how to convert it to 3D. After that, I will briefly show some other features.

No attempt is made here to teach all of ChemSketch. The idea is to guide you to some basics. If you can do the things shown here, you should then be ready to pursue more features of the program on your own -- as you need them. 

want to know how to get and install chemsketch??

click here

getting closer to CHEMSKETCH

1.1 Objectives

• How to start the program; • How to set and change file associations; • How to set default directories; • Basics of the ChemSketch interface, namely, the Structure and Draw modes; and • How to exit ChemSketch.

1.2 Starting ACD/ChemSketch

Once ACD/ChemSketch has been installed on your computer, follow these basic steps to start it: 1. Start Microsoft Windows. 2. Double-click the ChemSketch icon. –OR– From the Start/Run menu in the Windows 98/2000/NT/XP/ME/Server2003 taskbar, choose ACD/Labs and then choose the ChemSketch icon. –OR– Double-click the program file CHEMSK.EXE in the folder where you have installed all ACD/Labs software. By default this is ACD8. –OR– If you have other ACD/Labs programs running, from the ACD/Labs menu, choose ChemSketch. 3. You should see an opening splash screen. If this is the freeware version, you will see the ACD/Labs Products screen. Click OK to close it. If you wish to suppress this dialog box for the subsequent startups, from the Help menu, choose ACD/Labs Products and clear the Show this Screen at Startup check box.

*excel*

What is Microsoft excel?

Microsoft has enhanced Excel® in many ways to help build spreadsheets easily and reliably. Every one of us has made spreadsheets for a wide range of applications ranging from sales forecasting, to a scorecards for fantasy football. In order to build our model, we first conceptualize what we need, familiarize ourselves with the necessary algorithms and methods, and then build it in Microsoft Excel®. During this process, we have to be careful not to insert errors or disturb the model’s integrity as we define layouts and write formulas. When projects get large or complex, building spreadsheet applications can be challenging and time consuming.

Example of data using microsoft excel

Temperature	Percentage injured
8.0	4.7
22	12.3
15	6.5
13	5.9
12	6.6
21	10.3
20	8.4
9	4.0

Maple, first released in 1981 by Waterloo Maple, Inc.,
http://www.maplesoft.com
is a system for doing mathematics on a computer. Maple combines symbolic
manipulation, numerical mathematics, outstanding graphics, and a sophisticated
programming language. Because of its versatility, Maple has established
itself as the computer algebra system of choice for many computer users including
commercial and government scientists and engineers, mathematics, science,
and engineering teachers and researchers, and students enrolled in mathematics,
science, and engineering courses. However, due to its special nature and sophistication,
beginning users need to be aware of the special syntax required to make
Maple perform in the way intended. You will find that calculations and sequences
of calculations most frequently used by beginning users are discussed in detail
along with many typical examples. In addition, the comprehensive index not only
lists a variety of topics but also cross-references commands with frequently used
options. Maple by Example serves as a valuable tool and reference to the beginning
user of Maple as well as to the more sophisticated user, with specialized needs.

Examples of Numerical Calculations and
Built-In Functions:

calculate (4)(56)	4*56
simplify(8ˆ(2/3))	4

~MAPLE~

Maple, first released in 1981 by Waterloo Maple, Inc., http://www.maplesoft.com is a system for doing mathematics on a computer. Maple combines symbolic
manipulation, numerical mathematics, outstanding graphics, and a sophisticated
programming language. Because of its versatility, Maple has established
itself as the computer algebra system of choice for many computer users including
commercial and government scientists and engineers, mathematics, science,
and engineering teachers and researchers, and students enrolled in mathematics,
science, and engineering courses. However, due to its special nature and sophistication,
beginning users need to be aware of the special syntax required to make
Maple perform in the way intended. You will find that calculations and sequences
of calculations most frequently used by beginning users are discussed in detail
along with many typical examples. In addition, the comprehensive index not only
lists a variety of topics but also cross-references commands with frequently used
options. Maple by Example serves as a valuable tool and reference to the beginning
user of Maple as well as to the more sophisticated user, with specialized needs.

Maple™ is the essential technical computing software for today’s engineers, mathematicians, and scientists. Whether you need to do quick calculations, develop design sheets, teach fundamental concepts, or produce sophisticated high-fidelity simulation models, Maple’s world-leading computation engine offers the breadth, depth, and performance to handle every type of mathematics.