Lessons

Assalamu’alaikum my dear readers.

How are you feeling? It has been a while since I last updated this page. Well I am an avid reader not a keen writer.

In our last class of Computer-Aided Drug Design, we were assigned with a task to explain what we learned and how much we understood from all those software.

Okay here goes.

Since we had no basic what-so-ever in CADD, our lecturer decided to teach briefly about Bioinformatics. In the first class, we were taught in sequence analysis by using NCBI and MEROPs is used to search organisms name based on its peptidase (ClpP and Lon). We were asked to find any random 5 organisms for each type of peptidase and paste it in worksheet.

Unfortunately, due to my sitting position I heard it wrongly and I thought it was only 5 organisms for both peptidases. The table comprised of organism name, protein sequences, peptidase unit, active sites and its MEROPs ID.

Then using BLAST, we were taught to find its function, percentage identity and sequence. All needed to be done was copy and paste the protein sequence in Protein BLAST then choose PHI-BLAST.

Consequently, for the second class we were taught on how to use 2 programs namely ClustalX and Artemis. ClustalX is used in Phylogenetic while Artemis for genome sequence which can be found in SANGER website.

In ClustalX there are 2 outputs that can be obtained. Firstly, it can gives alignment of different microorganisms while another function is cluster tree or TREEVIEW. Basically TREEVIEW is utilized in observing the clustering of microorganisms into same or singular branch (the relationship between the microbes).

Single cluster denotes no similar branch with the microorganism, only one and it has no similarity in sequence and highly conserved. For multiple clusters, it denotes that some microbes are in the same branch and have similarity in sequence.

To practice, we were asked to do it using ClpP and Lon from the previous class.
For Artemis, the amino acid sequences were copied from the same notepad (ClpP and LonA) then it was pasted in Navigator for ‘Find Amino Acid String’ column and ORFs in range was marked and unwanted sequence was deleted.

At the end of the class we were asked to find FASTA sequence of 1TYF using ‘Protein BLAST’ in protein data bank or pdb form.

Last but not least for last week lesson, we were told to use RasWin software using 1TYF.pdb file to view the protein structure in molecular level. There were many forms of presentation such as ribbon and ball and stick. Also there was multiple color representing the type of protein structure (alpha or beta-pleated sheet).

Then we advanced to introduction of CADD which comprised of calculation and equation which normally learned in Physics. There are Molecular Mechanics, Molecular Dynamic, Quantum Mechanics and Energy Minimization Theory.
Since I am quite slow in this part, I won’t explain it further. I guess that’s all.

C’est la vie~

remarkable~

Supposingly, the ‘remarkable’ part of a person stuck at his back, just like an Umeboshi plum to an onigiri. He couldn’t comprehend how remarkable he is but others could. Feeling that he’s an ordinary person, jealousy erupts towards others.
Honda Tohru, Fruit Baskets anime.

Remarkable huh? I wonder if I could achieve the feeling. Mada mada dane I guess. Being my usual self sometimes, it exasperates others. I DO like to tease them. (Yeah I know! :P)

I can talk very fast that it made my ‘adik’ said, “Whoa! Hold your horses! Are you trying to catch a plane or something? You talked like a Shinkansen.” LOL! Oh the joy! He always feels incensed by the way I talk so fast. Do I really? I thought most people can keep up with my speed. Hee!
Talking about remarkable, I always feel that compassion or empathy is the most remarkable quality. Don’t you agree? I like to understand people. So much that my kin always told me off. (Duh! I was reading them. :P)

I love watching anime. The drove some of my friends crazy though cause the thought it is a child genre and inappropriate for someone my age. In debating the issue I told her that I couldn’t stomach a plot that comprised of greed and jealousy so much that people are slaughtering each other to obtain something (wealth, etc you name it) like most telenovela or local drama shows.

Yeah, it’s just a story but wouldn’t all those things corrupt naiveties of kids? More often than not they think that media gives the perfect impression of plausible behavior. Compassion my dear friends! Someone might say something like karma. What goes around comes around. I for one believe in equality. Give others the same modicum of respects you wanted for yourself. Then only you’ll be granted with the same.


‘Kay! Now I’m jabbering. Yada yada yada..

I’m VERY sure you guys have noticed the excerpt I wrote aforementioned. Well, you must be blind not to discern. ;)
I always think that everybody is unique. But do you realize that you ARE unique? Not in a appalling way for sure. Just being an individual instead of a copycat. During my adolescent years, I always strived to emulate my clique. I was being insecure and felt that if I don’t stick out for being myself then I wouldn’t be mocked for my eccentricity. Then, I decided that it doesn’t matter. Yeah! I still made some haphazard things. I feel happy enough though. As it is my walk, sloppy as it seems I manage to reach the destination. Right? 

Love yourself first then only you can love others. But for me, my self-esteem is coming from being loved. When people love you, like you or even adore you then only you learn to care about yourself. Cause you know you’re loved and it hurt them that you adopt devil-may-care attitude.

Enough of my lalalala~
C’est la vie.

Journey of my life~

Okay here goes.. I am so not a writer.. More of a talker I guess.. LOL~

My life..

Well basically I was born in PJ. I spent my early childhood in Kelana Jaya. Then my parents moved up to Subang Jaya when I was 4 or was it 3? Nah, that was my brother. I have been in Subang Jaya for as long as I can remember. Where was I? Oh right, education. I've been to normal what you called as 'sekolah kebangsaan' and never been to hostels except when I was in matriculation years at PJ.

Then after a year and half there, here I am in Kuantan. I've been here since end of 2006. I guess that was about everything.

About my FYP..

I am currently researching on Pharmacological activity of crude methanol extract of Sapium baccatum.
It is actually to observe the response of rats and mice to this extract and see if there are any contraindications.

Well, we meet again soon.. Insya Allah.
C'est la vie~