XML

 XML

 
XML TABLE

Molecular Mechanics	Semi Empirical	Ab Initio
Very Fast Speed	Fast Speed	Slow Speed
Restriction Parameters	Good Accuracy	Very Good Accuracy
Very Good Protein Modelling	Good Protein Modelling	Best Protein Modelling

XML DOCUMENTS

<Computational method>

< Molecular Mechanics=”Very Fast Speed”>

      <Semi Empirical>Fast Speed</Semi Empirical >

      <Ab Initio>Slow Speed</Ab Initio >

< /Molecular Mechanics>

< Molecular Mechanics=”Restriction Parameters”>

      <Semi Empirical>Good Accuracy</Semi Empirical >

      <Ab Initio>Very  Good Accuracy </Ab Initio >

< /Molecular Mechanics>

< Molecular Mechanics=”Very Good Protein Modelling”>

      <Semi Empirical>Good Protein Modelling</Semi Empirical >

      <Ab Initio>Best Protein Modelling</Ab Initio >

< /Molecular Mechanics>

</Computational method>

XML TREE
 

ProTein DaTa BaNk..(^_~)

Bismillahirrahmanirrahim..


I'm just finishing up my class in

 Computer of Science,

 and I was surprised when

 I recently got a task about PDB. 

However, it was 

quite interesting learning

 this challenging subject because

 I learnt new thing

 how to create a very  unique picture

 of Protein Data Bank.

Have you ever seen this picture??
It is about the image of Protein Data Bank.
Let us see what contains behind it!=)

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.^[1]

EXAMPLE OF PDB STRUCTURE

STRUCTURE OF HUMAN GUANOSINE MONOPHOSPHATE REDUCTASE GMPR1 IN COMPLEX WITH GMP




MOLECULAR DESCRIPTION

Classification	Oxidoreductase
Scientific Name	Homo Sapiens
Structure Weight	161576.49
Type	Polypeptide (L)

 That's all about PDB that I can share with you all.
TQ =p

..PoWer of ExCeL..

SAlam..=)

Here I wanna share with you about my Excel Assignment.

I have summarized what i did in the last class in this post.

P1

P2

T1

T2

Here are some features about what contains in this assignment:

Year	Housing Starts
1990	1.19E+06
1991	1.01E+06
1992	1.20E+06

For more details, you can visit my friend's blog,TQ..(^_^)

CHeMsKeTcH..(~_^)

Assalamualaikum..=P

Nice to meet you all again!

Have you ever heard about ChemSketch???

I'm sure there will be only certain of you that

already know about it.

However, let us see what it is actually...=)

ChemSketch is about the basics of 

structure drawing,
which occurs 

only in Structure Mode.It gives

the overview of the
chemical drawing features.
It really used in designing picture
of apparatus, 
chemical molecules and many more 
that hard for me to describe. 



In order for you to work 
efficiently in drawing,
you need to know some basic features of drawing
in this software:

Title bar	Shows the name of the program and the name of the currently open file
Menu bar	Contains a series of words. Each word links to a list (‘menu’) of related commands for working in the ChemSketch window in Structure mode
ChemBasic toolbar	Optional and contains Goodies  or other ChemBasic applications
Color Palette	Allows you to quickly color atoms  and bonds in the selected chemical structures

Here are some examples of what I havedone using ChemSketch

in the Computer of Science class:

Drawing lipids and micelles

 Drawing diagram of vacuum distillation apparatus


For more information that you want
to share with me,
please contact me using this blog or through my email, valianthourie@yahoo.com.
Thank you..=P

SMILES..=)

..Bismillahirrahmanirrahim..

Now, I learn more about what contains
in the Computer of Science
subject which provided by
International Islamic University Malaysia.
When looking at the title above, i really 

think that it

means S.M.I.L.E.S  like what we heard 

and understood before this.

But actually, S.M.I.L.E.S here bring

the meaning of 

Simplified Molecular Input Line Entry System 

The term canonical SMILES refers to

the version of the SMILES

specification that includes rules 

for ensuring that each distinct chemical molecule

has single unique SMILES representation.

The term Isomeric SMILES refers

to the version 

of the SMILES spesification

that includes extensions

to support the specification 

of isotopes, chirality,and configuration

about double bonds

Here are some SMILES Bonds

Single	-
Double	=
Triple	#
Aromatic	:

Below are the examples of SMILE notation:

 

For more details about this post,

I would like to suggest you to visit this blog.

Thank you(^_~)

Maple

                                              Bismillahirrahmanirrahim..(^_~)

(^_^)  MAPLE   ????

Anyone will feel like crazy while facing with mathematics.

Although some people feel that it makes trouble for them, someone will realize that mathematic is really an interesting subject..It really enjoyable if we know how to apply maple programming while doing mathematics using computer. Maple is a simple programming language, which means that we can easily write our own functions and packages.

Here, I want to share about what i have learnt in Maple programming. There are some interesting contents in Mathematics that can be apply using Maple programming.

• Numerical Calculations
• Basic Algebraic OPerations on Expressions

• Naming and Evaluating Expressions

• Implicit differentiation
• Using graph and tables to predict limits

It really an advantage for those who are interested in this Maple programming to score in KOS1110. You may put your target according to the IIUM grading system as written below, to make sure that this subject can contribute well in your CGPA.(^_^)  

Percentage Score	Letter Grade	Quality Point Equivalent	Remark
85-100	A	4.00	Excellent
75- 84	A-	3.67	Extremely Good
70- 74	B+	3.33	Very Good

Before I end this post, let me wish best of luck for those who will be taking this subject in the next semester. For more useful information about Maple programming, you can visit this link.

Enjoy your study with this challenging and interesting subject!(^_~)

BarakAllahufikum,wassalam.