lets learn CADD

Posted on Saturday, January 9, 2010 by shazwani

CADD or in its full and long name called as computer aided drug design. 1 credit hour subject that i have to take in this final sem otherwise i cant graduate..hahaha..very huge impact..

The course was tought by a very beautiful and nice lecturer, Mdm Norhaslinda.. this course is subjected to the aplication on computational methods where the knowledge can be applied in designing drug..

in the first class i learned about how to search for protein sequence from MEROPS, the peptidase database.
The summary page describing a given peptidase can be reached by use of an index under its Name, MEROPS Identifier or source Organism. The Summary describes the classification and nomenclature of the peptidase and offers links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.

The MEROPS database uses an hierarchical, structure-based classification of the peptidases. In this, each peptidase is assigned to a Family on the basis of statistically significant similarities in amino acid sequence, and families that are thought to be homologous are grouped together in a Clan. There is a Summary page for each family and clan, and these again have indexes. Each of the Summary pages offers links to supplementary pages.

For instance domain peptidase for CLPP and Lon. the sequence is very unique to a particular organism and present with its own merops id number. for example MER12345..once the number is clicked,it will pop out the respective sequence for the domain chosen before and also a description related to the protein sequence..

example of Lon peptidase sequence for MER060788

next, we need to blast the sequence on the ncbi website.
Open NCBI website and click Blast. Go to protein blast and blastp. Copy the Merops ID of Lon with the sequence from the notepad to the box. Choose for Protein Databank protein (pdb)

after that, click blast and it will give the band sequence of the organism. the first red sequence shows the highest similarity to the data sequence from the data bank.


next class, i learned about CLustalX and artemis, also protein blast from protein data bank. ClustalX is a software where several peptidase sequences are clustered and aligned together. the peptidase sequences are obtained from the merops website earlier.

open the clustalX folder and then loaded the sequences..next click do complete alignment in order to aligned all the respective sequence.
the sequences will be aligned according to the similar nucleotide sequence for the different organism.

aligned sequnces of several organisms

Clustalx also enable us to view the hierarchy of the organism by the Tree view option.

artemis is a software that can be used to visualized sequence features andthe results of analyses within the context of the sequence, and its six-frame translation. In order to view the sequence, Artemis requires Java software.

The BLAST from pdb file can be use to analyze similar 3d structure. the 3d structure can be viewed with another software name RasWin..from this software,we are able to view several modification to the 3d structure such as structure of ribbon,temperature of the molecule and it gave different color for different atom and chain or bonding.

3D view from RasWin software

i hope you guys can get a general view and benefited from it..i'll keep update this entry if there smthing i need to add up later on..

`its all about wani...

Posted on Sunday, December 13, 2009 by shazwani


Let me tell you something about a girl named Nur Shazwani a.k.a Wani Chomel..(i was forced by her to write this...*vomitting*)

err...Basically, i am her lab partner for FYP and obviously, this is Faroha writing this post..*ehem ehem!*

From my observations, she's (wani, who else..) a hardworking person..(so do i..hahaha!!) we've been working on our FYP since last semester. plus, since last friday we were spending our days and times in the lab, waiting for the column chromatography to separate our samples... and for your information, we have been in the lab from early morning till late midnight...*phew~*
and today, 14th December 2009, we officially completed our 1st separation... i repeat, 1ST separation...it means, there's more...(huh!!!)

eh...wani just remind me to write about her, not on FYP.. "okay wani...your wish is my command..."

ok..erm...other than being hardworking, she's no longer available...(guys out there,TAKE NOTE!!). the lucky person who is in love with her, no other than himady..(i don't know much about him,so i'll pass..)

next, she lives in Tmn Melati, near Putra LRT. She also longing to have a new handphone because if you see her phone now, you'll be suprised how she can manage to contact you with its current state... its okay wani, year end sale is just around the corner. Happy shopping okay! ^_^

i don't know what else to write because its not about me...if you want to know about me, feel free to visit my blog, and dont forget to click the ads okay...thank you!



Posted on by shazwani

Isolation of phytochemical from Henckelia sp. the topic of my final year project..this research is a basic research where the phythochemicals or constituents contain inside the plant need to be identified..i have to fractionate,isolate and lastly figured out the compounds name, MW, chemical structure and so on..of course i'll be using the machine to analyze all the compounds (identification)..and up to now,i'm on the phase of isolating the compounds..one more big phase to go ..hehehe..hope i can finish this project in within this year..so 2 more weeks left..chaiyok..hahaha..

Blog @ Blocked @ Black out???

Posted on Saturday, December 12, 2009 by shazwani

Finally...i have my own blog..credit to wan nur because she help me in dong this blogging stuff..i never know or have any idea how or even dream to have my own blog..until one fine wonderful day,mdm norhaslinda asked all of my classmates to create a blog and send her the URL's..huhhh..hmmmm...and last night,officially this blog was created..hahahaha..well done Shazwani Wani..

at moment i've no idea what to write..right now, i am still in the lab working on my FYP..the whole weekend spent here from early morning till late night..what a very hardworking girl =) ..since last friday and now its already sunday, i've been working with my lab partner,faroha, doing the column chromatography technique for isolating our samples..it was a very long process and i have to wait and collect every single drop of the fractions..again DROPS not a flow of stream..sigh..

this morning like few days ago, we came to the lab continuing the column process..working like usual collecting the drops, labelling the bottles, washing the beakers and also facebooking and chatting..hehe extra works added..the lab seems to be like before..nothing interest happen..people busy with their works until one incident happened to me..i thought maybe it is because of two and a half days of nonstop working..the story begun when i tried to call my 019 phone number using my other 013 number( second phone number)..then the phone rang and i picked up the phone without even looked whose the caller..

me :hello..hello..( trying to control the voice..as if the caller is a guy)
me :hello..hello..helllooooo..
caller:................ ( line was not very clear)
me :helllooo..

i kept saying hello but no answer replied..so i hang up the phone. i thought maybe the line there was not very clear and perhaps the caller will call me back later..but then i remembered something and i looked at my second phone..Call ended Total call: 00:09. dushhh..hahahaha how come i forget that me myself was the caller..no wonder there no answer from the other side..astaghfirullah wani..short term memory loss then..

Moral of the story:
i need to get enough rest and sleep..total two and a half tired days of worked causing blocked in some of my neuron pathway..chemical messenger cannot be sent to the right site making me half conciousness for 00:09 seconds..hehehehehe..that's all for my first blog entry..i'm writing this all out before me turn blackout( sleep)..hehe